When the Doctor Dreams
by biomechanical
Summary: Traveling alone, the Doctor sets the TARDIS to random and lands on Earth where he finds the human race enslaved by the Machines. Can he rescue mankind, or will he become a permanent addition to the Matrix? No slash. DW post-S4, Matrix Reloaded. AU.
1. Chapter 1

**A/N: When the Doctor lands on a twenty-second century Earth he doesn't recognize, and he finds the human race enslaved by the Machines, he embarks on an adventure to solve the mystery of the identity of the Source and how this time lime came to be. **

**This story can take place anytime after DW S4 "Journey's End" but before "The End of Time", of course, and starts in Matrix Reloaded. The T rating is a just in case, I never know how to rate these things.  
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**I do not own Doctor Who or Matrix.  
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**Reviews are lovely and happy reading!**

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><p>The Doctor sat on the bench with his feet resting on the edge of the console, knees slightly bent as he leaned forward studying the readouts on the monitor. He had set the TARDIS on random. He didn't know where she was taking him and he didn't care. He was alone again and this time he wanted to be alone. When he thought of how he ruined the lives of those who travelled with him, he almost couldn't bear it. He needed a distraction.<p>

The circular language of his native Gallifreyan shifted methodically on the screen that threatened to loll him to sleep, but then something caught his eye and he perked up. The Time Lord realized that the TARDIS was landing, and it was somewhere curious indeed. "Well, ol girl," he spoke to the console affectionately, "where have you taken me now?" He checked a gauge and frowned. "Twenty-second century Earth, eh? Huh. Nothing much interesting happened then. Guess I'll have to see for myself."

He hopped gingerly off the bench, strode for the door and held it open as he stared out in surprise. Taking a step outside and closing the door behind him, he let his eyes wander over the massive cavern that was artificially made, and at one point must have been in better repair. The whole of the tunnel was uneven, parts of it collapsed and filled with the clutter of twisted metal pieces and other debris.

The Doctor drifted further away from the TARDIS as he examined random bits of debris using his sonic to determine information about them. "Standard Earth materials," he spoke aloud to himself, "iron, steel, plastic. Nothing extraordinary." He sniffed the air and frowned. He licked the tip of his finger and held it up in the air. His frown deepened. Mentally, he confirmed that he was indeed on twenty-second century Earth.

"But this isn't right," he said, baffled. He turned on his heel looking over the cavern once more, "I remember a completely different twenty-second century Earth. What is going on here?"

A faint sound echoed from further down the cavern. The Doctor turned his ear toward the sound, leaning just a bit, and likened the buzzing to a swarm of bees. The buzzing grew steadily louder and the Doctor held his ground allowing his curiosity get the better of him. Finally, he saw the source of the buzzing rapidly flying toward him. The creature possessed a spattering of red glowing eyes set in a black orb-like body with numerous black tentacles flowing behind it.

"Well," the Doctor whispered in fascination for he had never seen anything like this before, "what do we have here?"

The squid-like creature, a robot the Doctor realized as it got closer, came to an abrupt stop and hovered roughly fifteen feet away from him. It whipped a tentacle around in front of itself with machine precision and the tip spun open into a dish shape. The Doctor watched as the robot appeared to be scanning him. "Hello, there," he smiled a friendly smile, even though his instincts were already telling him to run. "I'm the Doctor," he said. The squid closed the dish, moved that tentacle to the rear, and brought two tentacles to the front. The ends of these split open into claws. The machine advanced on the Doctor with terrifying speed, who bolted for the TARDIS.

The Time Lord managed to get his hand on the TARDIS door when the claw of the machine grabbed his arm, clamping down painfully, and stopped him in his tracks. He screamed out in pain, but twisted around and shoved the sonic in his free hand toward the face of the machine. The sonic chirped to life and the robot shuddered, its grip on the Doctor's arm relaxed. He yanked his arm free and pressed himself against the TARDIS as he kept the sonic aimed at the machine. Finally, the machine fell to the ground with a thud.

Since he expected the cavern to be silent with the fall of that machine, he was surprised to still hear the buzzing. He looked up and saw another squid machine hovering above the TARDIS. The Doctor aimed the sonic and the robot slowly shuddered as it drifted to the ground. But there was still more buzzing as yet a third machine flew around from behind the TARDIS with two tentacle claws aimed for the Doctor.

He knew he was out matched, so he snapped his fingers. The TARDIS door opened, but a mechanical claw dug into his right shoulder and yanked him back. He yelped in pain and struggled to aim the sonic at his captor. Instead, his arm was held fast by another claw that clamped around his forearm. The sonic fell from his fingers as he was abruptly lifted off the ground.

Before the Doctor was whisked away, he spied a glance at his beloved ship and saw her door slam shut on its own. He knew at least she would be safe, for the moment.

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"We're almost to broadcast depth, Neo," Link reported happily from his pilot's seat on the Nebuchadnezzar. For him, it was another day helping the One.

Neo stood behind Link and patted the pilot's shoulder. "Thanks," Neo said in an even tone.

"Anything for the One," Link said with a smile.

Neo felt fingers slip into his hand and he looked over his shoulder into the smiling, loving face of Trinity. "Are you ready?" she purred into his ear and pressed her body against his back. Neo turned to face her and wrapped an arm around her waist.

"Ahem," a deep voice said clearing his throat. Neo and Trinity turned their heads and smiled sheepishly at Morpheus like teenagers caught by a parent. Morpheus just looked on them with pride, enjoying the sight of young love despite the world they lived in.

"Alright, boys and girls," said Link in amusement, "Here we…hang on. What's this?" He stared at the monitor with crunched eyebrows. Morpheus, Neo and Trinity moved closer to take a look.

"What is it, Link?" Trinity asked with a clenched jaw.

"I'm getting an energy reading," he said.

"Squids?" Morpheus asked with concern.

"No. Not them," he shook his head and looked out the hovercraft's windows. "Let me get this girl down," he said and maneuvered the Nebuchadnezzar to a landing on the cavern floor.

"What. Is. That?" asked Morpheus staring out the windows in disbelief at a blue box with softly glowing windows that was very out of place amongst the dirt covered debris.

"Police box? I've never seen anything like it," Trinity whispered turning to Neo, "Have you?"

Neo shook his head and simply said, "No."

"You say that thing has an energy reading?" Morpheus asked Link.

He nodded his head, "Yeah. What do you want to do?"

Morpheus sighed in thought as he pondered the answer. "Take a closer look," he said at last with a shrug and disappeared into the rear.

Once outside, the trio cautiously approached the blue box. Neo held back, while Morpheus dared to reach out a hand and press his palm on the wood of the door. "It feels…warm," he said and tried the door. He frowned when it didn't give way. Trinity noticed a shining metal object on the ground that seemed out of place. She picked it up and examined the strange cylindrical object. "Look at this," she said and held it out for Morpheus and Neo to see. Neither of them knew what to make of it and Neo motioned to head back to the hovercraft. Trinity tucked the cylindrical object into a pocket and returned to the ship.

When Morpheus, Neo and Trinity returned to the bridge, Link asked, "Well?"

"Whatever it is, we can't open it," Morpheus answered, "We'll have to look it over back at the Dock. Right now, let's not waste our time. Neo has some saving to do."

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The Doctor stared grimly at the scorched world of the surface as the machine that carried him flew quickly through the air. It joined a stream of countless other squid machines like itself. The Doctor was horrified at their numbers. Must be billions. He noticed the sky above cracked with lightning and rumbled with thunder, and knew it wasn't a natural storm. It was something worse, a scorched sky.

The pain in his shoulder intensified each time his captor altered course, and he turned to biting his lip to keep from crying out. Finally, the machine brought him to a platform on top of a tower hundreds of stories high. The squid slowed as it approached the edge and released its grip. The Time Lord dropped to his knees as soon as his feet hit the grated platform. He rubbed his shoulder and waved his arm in circles to work out the pain.

"Doctor," a synthesized voice spoke smoothly.

Raising his head, the Doctor gazed upon a human-like face made up of hundreds of squid machines squirming in constant motion forming a wall of sorts that towered above him. He climbed to his feet, wincing at the pain in his shoulder. The wind that cut across the platform threatened to knock him down as it whipped around him.

"Yes, I'm the Doctor," he yelled over the wind, "And who are you?"

"You are species, Time Lord," it ignored the question, much to the Doctor's chagrin, "Estimated lifespan, seven thousand years. Energy output, one hundred times that of a human being. Doctor, known throughout the universe as the protector of Earth."

"How do you know those things?" the Doctor demanded, "You can't be of this planet if you know those things. Am I right?"

"You are correct," the face answered, "I am not of this planet but this planet is where I am and it is mine."

"What you have done here is in direct violation of galactic law!" the Doctor was outraged.

"Yes it is," the face replied nonchalantly, "In order to prevent you from alerting the Shadow Proclamation, you will be taken to power grid forty-two and inserted into the Matrix."

As a squid broke away from the face and flew down toward him, the Doctor screamed in fury, "Now, hang on just a minute! You still haven't told me who you are?"

"I am the Source," the face seemed to smile.

"Never heard of you. Why don't you tell me who you really are, eh?" he asked trying to by some time to think of a plan. He took a quick glance at his surroundings, but nothing useful stood out. He really wished he hadn't dropped the sonic screwdriver.

"That is irrelevant," the Source answered evenly as the approaching squid grabbed the Doctor by the arms and flew him through the air toward what he supposed was power grid forty-two.


	2. Chapter 2

The machine carrying the Doctor descended into an immense cylindrical tower with orange pods lining its curved walls. As he approached a liquid filled pod, the Doctor realized the other pods contained human forms. A second machine whirred up to the Time Lord and began its procedure by stripping him of his clothes with a few calculated passes of a red laser beam. A bit startled by that, the Doctor struggled against the squid that held him, but it was no use. The squid machine dropped him into the liquid filled pod and flew away.

He landed with a slurping splash in the thick liquid, but he didn't have time to take any action, the machine that took his clothes held his arms over his head and with cold accuracy, inserted the required implants into his arms, back and chest. He screamed in pain and anger, his fury and frustration turned to panic when the machine's claw clamped around his head and he heard the sound of a drill.

There a few things in the universe that truly terrify the Doctor, and he just added this to that list. The machine drilled a hole into the back of his head and inserted a large plug. How he was able to maintain consciousness, he didn't know, but he felt the chill of a healing coma creep in as his body fought against the implants. The machine turned him around, his head hanging low, and unceremoniously shoved a hose down his throat. The Time Lord could feel tubes slide into his main respiratory system and down to his stomach.

Even though he gagged against the hose, he was beginning to lose consciousness. His vision blurred as the machine plugged wires into the implants throughout his body. With a crunch and a click, a thick cable locked into place in the plug in the back of his head. His eyes closed as he was pushed into the thick liquid of the pod and darkness finally came.

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He opened his eyes and for a brief moment, he froze in panic and stared up at the ceiling. He had no idea where he was. Then as he looked around the room, his bedroom, he exhaled and relaxed. He was just lying in bed, his bed, in his apartment. It must be early morning since the daylight was just starting to filter in through the windows. There was a soft moan from beside him and he turned his head to see the back of a feminine form lying next to him.

Slowly, he reached out and gently rested his hand on her shoulder. Her name is Claudia, the thought popped into his mind. She responded by rolling over and looking at him with half open eyes. She smiled and purred, "Good morning." He maintained a neutral expression as he looked at her and he remembered the day he met her at the observatory and how she shared her hope of flying through the stars one day. When he said that was his dream as well, they fell in love.

Claudia's smile faltered slightly and she propped herself up on an elbow, her wavy dark brown hair falling around her shoulder. "Oh, John," she said in gentle concern, "did you have the nightmare again?" The nightmare, he pondered, oh yes of course. He nodded slowly while he organized the memories of his life that steadily streamed into his mind. Claudia leaned forward and gave him a gentle kiss on the lips. "Maybe you should call in today," she said, "Take a day off and get some rest."

What did he do for a living? Then he remembered, "No, I can't," he said with a slight frown, "I have patients today." He wondered if he'd always had an English accent.

"Ooohhh everyone wants to see Doctor John Smith," she giggled as she slid her fingers under the sheets, "You better call it an early day then because when I get home later, be ready." The word 'doctor' rang something in his mind, but it quickly faded away when he started laughing as Claudia tickled his side. As he tickled her in return, a part of him wondered if he had always been ticklish, or if this was something new?

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A short time later, Claudia left for work and John sat on the edge of his bed, thinking. He still struggled to shake the feeling that something wasn't right with…well…everything. Damn that nightmare. Even though he couldn't remember details of the dream, the emotion of it still lingered. Maybe a shower would help, he thought. He padded into the bathroom and stopped short when he saw himself in the mirror.

His short brown hair spiked out in all directions, and his large brown eyes that seemed to know so much more than they should, stared back at him. Didn't he used to look different? But that was a bit silly. Of course, he always looked like this. He needed a shave to get rid of that stubble, and he was rather tall and lanky, but fit. Like he could run, oh so very fast. He glanced at the clock, and he realized that if he didn't hurry, he was going to be late for the first appointment of the day.

After the shower, John headed to the walk-in closet and stepped inside. On one side was obviously Claudia's clothes, and the other side his. He let his eyes wander over the shirts and jackets that hung on his side, organized in groups. Button-up shirts in white, light blue, and light gray hung with jumpers in black, dark green and purple. The suit jackets included a brown pinstripe, a blue pinstripe, and a solid black, each with matching pants hanging on the hanger. Was this all he had? Time to do some shopping, he decided.

After considering what to wear, John finally decided on a white button up shirt and the brown pinstripe suit. Slipping into the clothes, he didn't linger over the ties, grabbing a burgundy one with a turquoise paisley pattern and draping it around his neck. He made a mental note to ask Claudia later about when he'd ever worn the red bow-tie since he couldn't remember it at all. Bending over to grab a pair of shoes, he paused to choose between black dress shoes and one of the three trainers, red, white, or black. He chose the white trainers in anticipation of being on his feet all day.

Finally John was ready to head to the hospital. He reached in the coat closet by the front door and paused at the sight of a long tan overcoat, black leather jacket and a green velvet coat. A quick glance at the sunshine though the window changed his mind about a coat, though he pondered taking the very long scarf that hung on the guest coat rack just in case, but decided against it. He patted his pockets making sure he had his keys, wallet and cell phone. Satisfied that everything seemed to be in order, he opened the door and entered the world.

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"Where did you say you found this?" Councilor Hamann asked Trinity as he closely studied the strange blue box now sitting on the Dock platform next to the Nebuchadnezzar. He tried the door, but gave up when it wouldn't budge.

Trinity, standing next to the Councilor, crossed her arms. "In the north grid tunnel at broadcasting depth," she answered evenly, and then she remembered what else she found. "Oh, there was also this," she held up a silver cylindrical object with a blue rounded tip for the Councilor to see.

His eyes lit up with curiosity and he gently took the object from Trinity's hand. Silently, he carefully examined the object. "It was on the ground next to that," Trinity spoke, "it stood out from the debris so I thought it might have something to do with the crate."

The Councilor nodded. "It very well may, Trinity," he said as he ran a finger down the side of the device. His finger hit a tiny button and the device lit up in his hands, startling both the Councilor and Trinity. They leaned in closer and listened to the steady pulsing sound it emitted.

A loading mech happened to walk in front of where the Councilor was aiming the device. The mech suddenly came to a halt and sank down as if it were turned off. "Hey!" the driver shouted in frustration, "What's the matter with this thing?" Trinity and the Councilor stared wide eyed between the mech and the device realizing that this tiny device can stop a machine cold.

Councilor Hamann smiled wide and he ran toward another mech with Trinity close behind him. He aimed the blue-tipped device and activated it. The mech reacted like the other and shut down. "This is amazing!" he couldn't help but sound quite ecstatic for an older man.

"We need to destroy it!" boomed the voice of none other than Commander Lock. Trinity and the Councilor spun on their heels and watched the Commander march up to the blue box with a hard scowl on his face. The Councilor rushed over to him. "Don't be ridiculous," he said with anger in his voice, "We don't even know where it came from, and this," he held up the silver device, "is a weapon against the machines."

"No, Councilor," Lock clenched his jaw, "we don't know where it came from, which is why we need to destroy it. It could be a trick, or a bomb, from the machines."

"Don't be a fool, Commander," Hamann pleaded, "why would the machines trick us with something that can disable them? I think that whatever this blue box is, its here to help us."

The Commander waved a dismissing hand at the Councilor and brushed past him. He barked an order for a loading mech to take the crate to the end of the docking platform. The Councilor shook his head as a mech did as ordered and took the blue box near the platform's edge. Trinity stood next to the Councilor and was joined by Neo and Morpheus. They watched a battle mech aim its cannons at the box and open fire.

The Dock echoed with the noise of high powered bullets pounding the box. The box did not shatter into pieces as expected. Instead, it rocked back and forth under the force of the bullets until finally it tipped over backwards landing on its backside with a resounding thud. The Commander yelled a cease fire and all present on the platform stood in awe of the box unscathed from the assault, save for a few paint chips. Even though it lay on its back, its still lit signs and windows glowed in defiance.

The Councilor shot a cocky glare at Commander Lock who stood with his mouth agape. Morpheus whispered that this had a prophetic meaning, and Trinity wrapped her arm around Neo's waist. "Time to visit the Oracle," Neo spoke at last.


	3. Chapter 3

**A/N: thank you for the reviews so far...I really appreciate them :)**

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><p>Neo flew high above the clouds leaving a trail of rippled distortion behind him. His long black overcoat whipped around him, but he didn't seem to mind. Even though none of this was real, a part of him did enjoy the feeling of freedom flying gave him. As he neared his destination, he descended from the clouds and headed for the roof of an old, brick building.<p>

When he planted his combat boots on the roof, the Matrix rippled out from beneath him as it worked to compensate for his impossibility. After a few moments, the ripples vanished and the roof top was the way it should be once again. Neo quickly entered the building through the roof access door and headed down the all too familiar stairs. When he reached the apartment door, he paused to take off his sunglasses, tucking them into a pocket, and slowly opened the door.

The smell of fresh baked cookies washed over him like a wave, and he breathed it in. He didn't need to call out for the Oracle, he knew exactly where she would be. When he stepped into the tiny kitchen, the Oracle looked up from her seat near the oven and smiled the kind of smile you would expect from a loving grandmother.

"Neo," she said sweetly, "So glad to see you again."

Neo stood at the kitchen entrance and clasped his hands in front of him. "It's nice to see you, too," he offered a small smile. He silently looked at the Oracle, and studied the orange code that made up her program. It was still the same.

"Well, I know you didn't come here for my cookies, though you're more than welcome to have one," she winked, "what can I do for you?"

"We found something in the tunnels near the surface," he started.

"The blue box?" the Oracle asked.

Neo paused in surprise, but it was fleeting. He was used to the Oracle knowing things when he didn't think there was a way she could. "Yes," he answered, "Do you know what it is?"

"Sadly, no," she said, "but it belongs to someone, someone who shouldn't be here."

Neo perked up at this news, "Who?"

"His name is hidden, not to be known, and he is a man of many faces," she slipped on an oven mitt, "but his presence in the Matrix is a grave error. One that changes everything."

"How?" Neo became a bit more tense than usual, "How does he change everything?"

The Oracle slid off her stool, opened the oven door, and pulled out a baking sheet covered in hot cookies. She took in a deep whiff and exhaled with a satisfied smile. "He knows things. More than you can ever imagine, but it's all sealed away inside his mind," she sat the baking sheet on top of the stove and resumed her seat on the stool, "Help him remember, Neo. Find him before Agent Smith does."

"But if you don't know his name or even what he looks like," Neo frowned and sounded slightly frustrated, "How can I find him?"

The Oracle just smiled that gently, knowing smile. "You will know him," she promised with a nod as she used a spatula to move the cookies to a plate, "An apple a day, Neo, an apple a day."

Neo's eyebrows crunched together because he recognized one of her cryptic riddles when he heard one, and it also meant that the conversation was over.

"Cookie?" she held out the plate of cookies with a bright grin.

He sighed and took a cookie, cherishing its warmth on his hand. He turned to leave the apartment and the Oracle called out in a voice as sweet as ever, "Come back again soon, Neo."

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"Doctor John Smith to ER! Doctor John Smith to ER!"

John was walking down the hospital corridor toward his office after a scheduled patient visit when he heard the announcement over the intercom calling him to the emergency room. Even though he was a general practitioner that regularly saw patients in scheduled visits, sometimes he covered as an ER doctor. Today was one of those days.

He spun around on his heel and jogged down the hall. He was glad he wore those trainers, his feet thanked him. Suddenly, he became aware that running seemed very familiar. Surely he'd run down these halls before, but no, this time it was different. Almost like he was being chased by something meaning to hurt him. That was ridiculous, he thought. Still, he turned his head and glanced over his shoulder. Nothing chased him. He brushed off the feeling and focused on getting to the ER.

As soon as John appeared in emergency, a nurse called him over to a stretcher bed where a bloodied body lay. He quickly glanced over the patient, who appeared to be wearing a policeman's uniform, and was appalled. He'd never seen anything like this. The young man's legs and arms were broken, in several places from the look of it, and dark blood oozed from the side of his head. The poor man looked like something literally chewed him up and spit him out.

"What happened?" he asked the nurse, a young girl fresh out of med school, as he rushed the patient into surgery.

"Car chase," the nurse answered, "Multi-car accident and some kind of brawl between the cops and this gang in black. It's been all over the news."

"Crunched up in a car, I take it?" John slipped into a surgeon's gown and scrubbed his hands.

"No," the girl said with a vacant tone, "They say that one of the gang members in a long black trenchcoat did this with his bare hands."

John didn't know how to take that. It was a bit of strangeness to add to his already strange day, so he chose to ignore what the nurse said and focus on saving that man's life.

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"An apple a day?" Trinity asked Neo after he met up with her and Morpheus in a vacant warehouse they deemed safe and he told them what the Oracle had said. "What does that mean?" she continued.

Neo shook his head, looking slightly solemn, "I don't know, but I have to find this man." He looked over at Morpheus, his friend, who sat in an old chair in the middle of the room.

Morpheus simply steepled his fingers and remained silent in thought. Trinity started for the door. "Where are you going?" Neo asked.

"Well, we can't just stand here," she whirled around, "if the Oracle says he's so important, we should be looking for him."

"But we don't even know where to start, Trinity," he said almost sounding like he was about to give up.

"Hospitals," Morpheus spoke smoothly and slowly stood up.

Neo and Trinity looked at him with questioning expressions. "Hospitals?" asked Neo.

"An apple a day," he said as he walked past the pair towards the door, "keeps the doctor away."

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Something was different in the Matrix. He could feel it in every fiber of his code. Something has changed, and it was something beyond the changes his newfound abilities had done. As Agent Smith stood on the edge of a skyscraper looking down across the digital city as if he were god, he slowly filled his lungs in a deep breath of air. He savored the feeling, even though he knew perfectly well that it wasn't real, just a simulation.

There was some thing, no, some _one_ out there who didn't belong, and he intended find that person. To own that person. Mentally, if it could be called that with him, he issued commands to his copies spread throughout the city, find the one who didn't belong.

Agent Smith smiled a dark smile knowing the copies instantly obeyed him and started their search. Soon he would have the answer, and he couldn't wait to find out what it meant for him.

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After several exhausting hours in surgery, John could not save that man's life. He'd seen death before, it was inevitable working in a hospital, but this time, it struck him harder than usual. John entered his office and sat a hot cup of tea down on the desk, then fell into his chair. The man's death wasn't supposed to happen. The thought repeated itself over and over inside his head, and he pondered what it meant. He absentmindedly picked up a spoon to stir the tea, when something frighteningly amazing happened, the spoon bent around in his fingers as if it were snake.

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Neo, Trinity and Morpheus headed toward the hospital closest to the warehouse only ten blocks away. The trio marched down the sidewalk and let the crowd part away for them pass. When the hospital was in sight, Neo paused on the street corner. Morpheus and Trinity stopped with him and waited. Neo closed his eyes a moment. "Someone's starting to wake up," he said and looked at the hospital. With a nod to each other, they continued.

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John threw the spoon away from, sending it clattering across the desk, and shrank back like it might bite him. With wide eyes, he watched the spoon snap back into its normal spoon shape. His heart pounded in his ears and his hands shook uncontrollably until he took a couple of deep breaths. Maybe he did need a day off, he thought. With a new found determination, he reached for the phone and called the scheduler, telling her to cancel his appointments until the day after tomorrow.

John jumped up from his chair, gathered his personal effects and hurried out the door. As he moved quickly down the halls toward the exit, he shivered in nervousness, but tried desperately to hide it behind friendly nods and smiles to those he passed.

Finally, he made it to the main lobby and held the glass doors that lead out to the street in a steady gaze as he made a quick approach. Three individuals, two men and a woman, walked into the lobby. They wore dark sunglasses and long back overcoats, and they paused, slowly turning their heads like they were scanning for something.

_They say that one of the gang members in a long black trenchcoat did this with his bare hands_, the nurse's words echoed in his mind and he stopped in his tracks. He held his breath as the trio decided to move toward the receptionist desk…away from the exit. Gathering a bit of courage, he swiftly moved through the people in the lobby and slammed into a glass door sending it flying open with a bang.

John's throat choked with fear and he found himself nearly running down the sidewalk. He had the feeling that he was being chased, so he chanced a look behind him. To his horror, the three in black were on the sidewalk walking briskly after him. He ran as fast as he could and tried to figure out what that gang could possibly want with him.


	4. Chapter 4

John crouched behind a Dumpster in an alley and tried to catch his breath. He was breathing hard, nearly hyperventilating, and sweat dripped off his brow. Why would those people want him? How did he know they wanted him? Somehow he just did. But why? He thought of his parents living in the suburbs just outside the city, he thought of his apartment and Claudia. Fond memories of her pretty smile and musical laugh helped calm him down.

He peeked over the Dumpster and dropped back down at the sight of the three in the black long coats standing at the entrance to the alley. They weren't looking down the alley, but one of the two men said in an even tone, "I've lost it. Whoever was waking up has fallen asleep again."

"Do you think it was him?" the woman asked.

"I'm not sure," the man answered.

"Let's check the other hospital," a deeper male voice said.

After a moment, John didn't hear their voices anymore and assumed they walked away. A quick check over the Dumpster confirmed this. With a sigh of relief, he stood up and ran to the other end of the alley. He couldn't wait to get to the safety of home.

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Agent Smith entered the lobby of a hospital and frowned at the stench of it. He hated these places where humanity smelled its worse. Still, he forced himself to inhale the air and avoid gagging at the unpleasant aromas. "The some one was here," he muttered to himself and headed deeper into the hospital.

Like a blood hound, Agent Smith strode down the halls until he found an office that interested him. He opened the door and slowly stepped inside. His eyes wandered over the small room and came to a rest on a spoon on the desk. He picked up the spoon and rubbed his fingers over its smooth surface noting that its code had been manipulated. Crunching the spoon into a small ball of twisted metal, Agent Smith opened his hand and let it fall to the floor without a second thought.

He read the name plate on the edge of the desk, John Smith, PhD. He snatched up a framed photo that depicted a woman with wavy dark brown hair and a wide grin resting her head against the shoulder of a scruffy haired man with soft brown eyes and a cheery smile. He slammed the picture onto the desk, cracking the glass.

Now he had a name and a face. A dark smile crept along Agent Smith's face as he turned on his heel and marched out of the hospital with a sense of unstoppable determination.

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John burst through the door of his apartment door and slammed it shut behind him. Leaning against the closed door, he sank to the floor in exhaustion. He needed to get a hold of himself and began breathing long controlled breathes. Drawing his knees up, he rested his elbows on his them and held his head in hands. He closed his eyes and he realized how so very tired he was, so he allowed his mind to drift away toward somewhere else.

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He felt at peace as he stared up at the stars and familiar constellations. His fingertips gently played across velvet soft grass. He turned his head and smiled at the sight of the beautiful red blades brushing against his skin. Sitting up, he stared out over the valley from his hilltop perch at the golden citadel off in the distance. He knew where he was and he smiled.

_Wake up_, a soft female voice whispered in his ear.

The voice didn't startle him for he knew she was an old dear friend that has been with him nearly his entire life. He turned his head and smiled lovingly at the blue police box standing just a few feet away. Her doors stood wide open, inviting him to come back home.

_Wake up, Doctor_, the sweet voice repeated with urgency.

Suddenly he was submerged in thick pink liquid, trapped inside a capsule just large for him to lie in. He panicked and wildly pounded on the walls of his prison with resounding thuds that grew louder and louder.

John's eyes flew open and he found himself lying on his side on the floor in front of his apartment door. Someone was on the other side, knocking with purpose. He jumped to his feet and rubbed his eyes before peaking through the peep hole. John stepped back, not liking what he saw on the other side; two twin men in white with white hair and black sunglasses. Something about them seemed menacing.

"What do you want?" John called out.

"A moment of your time," came the answer in a smooth voice.

"I'm, uh, busy right now," he said pulling out his cell phone and dialing 9-1-1, "Come back some other time."

Suddenly, a ghostly head appeared in the door followed by the rest of his body as the pale man stepped through the door. His twin followed close behind. The shocking surprise of such an impossible sight made John drop the phone and stagger back with his mouth agape.

"The anomaly," one twin said to the other as he stepped on the phone and crushed it under his foot. Slowly the twins advanced toward John, who found himself digging around the inside pocket of his jacket, but not knowing exactly what he thought was in there that could help.

"What do you want with me?" he pleaded as they each grabbed his arms.

"The Merovingian wishes to speak with you," the twins said in eerie unison.

.

.

Agent Smith stopped in front of an apartment door and smiled a rather smug smile. "Here we are, apartment two twenty-one," he said closing his hand around the door handle and using his great strength to force the door open.

The wood of the doorframe shattered and Agent Smith shove the door aside as he entered the apartment. He looked over every item, noting the crushed phone on the floor. He entered the living room where he saw a set of photos on the wall depicting the same faces from the picture on that desk. He knew he was in the right place, but Mr. Smith, and the agent did enjoy the irony of the name, was not in.

.

.

Neo stood with Trinity and Morpheus on the sidewalk outside a second hospital. They did not find what they were looking for, and their shared stoic expressions showed it. Neo closed his eyes and let his mind reach into the Matrix. He searched the code for something to stand out, and finally it did. He opened his eyes and turned toward a plain looking apartment tower not too far away.

He pointed to the building, "Meet me there." His lover and friend nodded once, then ran to a car and commandeered it, screeching its tires on the pavement as they sped away. Neo crouched down, bent the Matrix to his will and launched himself into the air. In a matter of seconds, he arrived at the apartment tower and quickly flew up the stairwell.

Neo noted the door to his destination appeared to be kicked open and cautiously entered the apartment. Looking through the Matrix code that made up all things, he saw a glowing pattern all too familiar standing in the living room.

"Mr. Anderson," Agent Smith smirked. The One frowned slightly and patiently waited for the agent to make a move. The cell phone in his coat pocket rang out and that was the moment Agent Smith chose to strike. Neo stepped to the side, grabbed the agent's arm and swung him into the back wall.

Through the hole that Agent Smith's body made as he crashed through it, Neo saw the agent slowly rise to his feet. Behind him, a man and woman who were sitting on a sofa watching television, warped and became two more Agent Smith's. The cell phone rang again, and the three Smith's dashed toward Neo assaulting him with a flurry of kicks and punches that he easily deflected.

The One grabbed an agent by the collar and sent him flying straight up crashing through the ceilings and floors of the apartments above. He sent another agent out the living room window with hard kick, and yanking the third agent by the arm, Neo flew out the window. The cell phone rang a third time. He swung the agent he held by the arm up and over, and then released him. The Smith flailed his arms and legs as he slammed helplessly into the other airborne agent. The two plummeted into a building and disappeared in a hole of dust, concrete and mangled metal.

Neo hovered in the air watching the agents below through the Matrix code. Satisfied they were no longer a threat, for the moment, he shifted his gaze to the street in time to see Trinity and Morpheus run from the apartment building. They jumped into their stolen car and screeched after a black SUV already several blocks away.

Flying through the air, Neo reached the black SUV and landed firmly in the middle of the street in front of the vehicle sending a ripple of distortion through the code around him. The SUV swerved around Neo as both albino twins ghosted through the vehicle with swords drawn.

One twin brought the sword down on Neo while the other rushed toward the oncoming car carrying Morpheus and Trinity. Bullets flew, swords were dodged and a twin ended up embedded in the brick facade of a building for a moment. But when the ghostly twins made a hasty retreat, Neo realized it was all a distraction for the SUV to make its escape.

Morpheus and Trinity climbed out of the car to join Neo at his side. "Do they have him?" Trinity asked.

"Yes," Neo replied evenly.

"What about Agent Smith?" Morpheus said and glanced over his shoulder toward the building where Neo threw the copies.

"He knows who he's looking for now," Neo said, "and so do I."


	5. Chapter 5

After demanding to know where he was being taken and having a gun shoved in his face as the answer, John sat in the back seat between the albino ghost twins in silence. Though, he couldn't help but let out a startled scream when a man in a long black flowing coat, the same from the hospital, suddenly appeared in the street right in front the vehicle. Thankfully, the driver was quick enough to swerve around him.

Once the ghosts left the vehicle, John was alone in the back seat, but the dark haired man in the front passenger seat was quick to draw a pistol and keep it trained on him. That was enough for John, and he chose to keep quiet and do as he was told. Anything to stay alive.

John was terrified as he watched the buildings, cars and people whisk by out the SUV window. His thoughts drifted to Claudia, wandering what she was going to do when she came home and found him missing. The blue police box flashed into his mind. He blinked it away. Claudia would probably call the police and hopefully he will be rescued soon.

The SUV entered an underground parking garage and screeched to a halt in front of an elevator entrance. The gun toting passenger climbed out of the vehicle and opened the back door, motioning for John to get out. He did as he was told and followed his captor, joined now by the driver, to the elevator.

The lift up was deadly silent, though John felt like he should be talking, saying something, anything, even something cheeky. However, the seriousness of his kidnappers prevented him from opening his mouth. Instead he considered his situation and wondered what kind of day it has been for him. Crazy. Pure and simple. Just what _was_ is it about Thursday's?

Finally, the doors slid open and John was surprised by the very high class room he was escorted into. It was an apartment, or hotel room for all he knew, but the tall floor-to-ceiling glass walls allowed for a beautiful view of the city. In the center of the large room stood a sleek black coffee table with two sofas of modern design facing each other in either side of the table.

On the sofa looking over the city, sat a man in a dark suit and slicked back hair. He was alone, but his bodyguards stayed nearby at a bar off to the side. He casually sat with an ankle resting on a knee and held a glass of wine in one hand keeping his gaze on the view before him. With a flick of his rest, the two men walked John over to the sofa opposite.

John lowered nervously to the sofa and swallowed as he looked at this man who was clearly in charge of whatever was going here. For a moment, the man simply stared at John with faded blue eyes and a neutral expression. It only served to make John even more nervous. The blue box flickered into his thoughts again, and yet again he pushed it away.

"So," the man spoke at last in a thick French accent, "you're the anomaly."

John couldn't help but be confused. "Anomaly?" he asked weakly.

"Yes. And I can't say that I'm impressed," he replied in disappointment, "Wine?"

Now, John felt insulted that overrode his fear a bit, "Who are you?"

"I am the Merovingian," the Frenchman rested the fingers of his empty hand on his chest as he spoke with a prideful smile. The driver of the SUV walked up to John and offered a glass of red wine. The unexpected gesture made John wary but he took the wine and simply held it in his hand.

"What is that supposed to mean?" John asked, "And why did you call me an anomaly?"

"Oh, but Mr. Smith," the Merovingian raised his eyebrow, "the question you should be asking is why are you here?"

"How should I know?" John retorted, "You brought me here."

"No, no, no!" the Frenchman shook his head and leaned forward. "Why are you here, in all this?" he waved his hand in circle, "What is your purpose?"

John, now frustrated, abruptly set the wine glass on the coffee table. "What are you talking about? I'm the doctor. That's my purpose," he blurted out without really realizing what he was saying.

The Merovingian gazed on John with an intensity that made John want to shrink back into the sofa. "_The_ doctor, not _a_ doctor? Curious," the Frenchman cooed thoughtfully.

_Wake up_, a barely audible female voice whispered in John's mind. Something familiar welled up inside him, but he mentally fought against it, struggling to maintain focus on the conversation he was having with this strange man.

"So, here I have before me is a confused anomaly that doesn't even know why its here," the Frenchman continued speaking aloud to himself even though he kept his eyes on John. "Why were you created? Why create such a progr…" he caught himself and his face lit up in realization, "Oh my. You're not a program at all, but some _one_…alien to the system…inserted into the Matrix. Yes! But why?" He leaned back in silent contemplation.

John didn't know what to make of the Frenchman as he glared at the man with confusion and fear. The blue box entered his thoughts and he remembered standing inside its golden control room flying through space and time. He shook his head. No, this fellow was crazy, but a part of John could no longer deny that the Merovingian was right, and that thought scared him most of all.

The SUV driver approached the Merovingian from behind the sofa and whispered something in his ear. The Frenchman smiled and jumped to his feet, "Ah, it appears I have a guest." John decided to stay where he was unless he was told to do otherwise.

The elevator dinged and its doors split apart. The Merovingian's smile fell to smoldering anger at the sight of the men stepping out of the elevator. To John's astonishment, the five brown suited men were identical. "Agent Smith times four," the Frenchman hissed, "What are you doing here?"

The agents brushed past the Merovingian toward John. "Out of my way, program," one of the agents said as they passed, much to the dismay of the Frenchman, who seemed greatly offended at being called a mere program. John didn't like the menacing faces on the agents and looked around like a frightened animal for a place to run. He was trapped.

"Hey, hey, hey!" the Merovingian said as he moved in front of the agents and held up his hands, "He's mine." One of the agents took a step toward him and the Frenchman flicked his wrist.

Chaos erupted. The Frenchman's bodyguards held up uzis and opened fire peppering the agents with a rain of bullets. One agent dodged under the bullets that slammed into another who was too focused on John. Two agents leaped into the middle of the bodyguards and delivered well placed punches. The Merovingian made a dash to the elevator and stood inside it frantically pushing buttons. John dove to the floor when the gunfire erupted and crawled into a back corner as fast as his hands and knees would take him.

He found himself examining details of the room, looking for something he could use to his advantage. He was fishing in the inside jacket pocket again like it was instinct for him to grab something that would help him from there, but the pocket was empty. He froze when he saw an Agent Smith stalk toward him with an evil grin on his face.

The gunfire ceased and John knew that the Merovingian's guards were dead. Agent Smith was joined by his four clones as he grabbed John by the lapel of his jacket with one hand and slowly lifted him to his feet. John was horrified at the strength of this terrible man, if that's what he was, and he struggled to break free from the iron grip.

"At last we meet, Mr. Smith," the agent grinned like a wolf, and lifted John off his feet completely. John grasped at the agent's wrist with both hands and flailed his feet trying desperately to free himself. The agent held his other hand straight and true, like an arrow, and pulled back his arm. John braced himself for the pain of the expected punch and closed his eyes.

John's eyes flew open as he felt the agent's hand slip into him. He opened his mouth to scream, but no sound came out. The feeling paralyzed him, terrified him. He felt like he was losing himself, like he was being erased. He thought of Claudia at first, but her face faded away when she suddenly wasn't so important anymore. The blue police box with her doors wide open beckoning him to return home was more important than anything of all.

The nearly musical sound of glass shattering into millions of pieces was deafening, and the agent paused with his hand embedded in John's gut to see the cause of the interruption. "Mr. Anderson," he hissed and pulled his hand free. He released his grip on John, who collapsed to the floor in a heap of choking and coughing.

The five Agent Smiths wasted no time launching themselves at the man in the flowing black overcoat, who coolly stood in the middle of the room with clenched fists. A punch from the man in black sent an agent flying at bullet speed out another window, shattering it on impact. A well placed kick stopped another agent cold, forcing him to double over to the floor. He grabbed the incoming fist of an agent, swung him around and slammed him into the other two agents sending them crashing through the nearby wall.

John watched the impossible fight with wide eyes, but stayed on his knees on the floor only because it seemed like the safest place to be. When there were no longer Agent Smith's standing in the way, the man that the agent called Mr. Anderson took several quick strides to John and held out his hand. "Come with me if you want to wake up."

Wake up. John remembered those words from his dream and he knew that he wanted to wake up, oh so desperately did he want to wake up. Looking at the fear, confusion and even anger on his face reflecting in Mr. Anderson's dark glasses, John took the offered hand. Mr. Anderson pulled him to his feet and led him to the broken window. Wrapping an arm around his waist, Mr. Anderson said, "Hold on."

John swallowed as he felt the breeze wash over him and he looked down at the street so very far below. He rested an arm over Mr. Anderson's shoulders and resisted the urge to cry out as they flew swiftly through the sky.


	6. Chapter 6

**A/N: I really appreciate the reviews, thank you everyone!**

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><p>John silently followed behind this strange man, Mr. Anderson apparently, down a dimly lit and dingy hallway that ended at a rusted steel door. Mr. Anderson gave the door a few quick raps with his knuckle and a small hatch slide open revealing a pair of eyes in sunglasses on the other side.<p>

The hatch slammed closed and with a dull grinding sound, the door slowly opened. Mr. Anderson briskly entered and John quickly followed. He glanced over the two men guarding the door, both wore different styles of leather outfits and dark sunglasses, and each carried large pistols. "Welcome back, Neo," one of the men said and Mr. Anderson gave a quick nod as he passed. When John passed, the two men simply watched him with cool gazes.

Mr. Anderson, or Neo rather, walked through a second doorway that opened into a large room of a derelict warehouse. The corners of the room were shrouded in darkness that gave the impression the room was smaller then what it really was. The only light was a single fixture hanging from the ceiling by its power cord. The bulb gave off a dim glow, but it was enough to create a circle of illumination in the darkness.

Two antique chairs sat facing each other in the center of the circle of light. A bald man that John recognized from earlier sat cross-legged in one of the chairs holding his fingers in a steeple. Next to him, stood the woman from the hospital as well. Neo walked up to the occupied chair and stood next to it opposite the woman. He held out a hand toward the empty chair. "Please sit," he said to John in an even tone.

John didn't see that he had much of a choice, so he sat and laid his hands on the armrests. He looked at the three in front of him and wondered if this was a good idea. After all these were the people who murdered that cop, right? _Wake up_, that feminine voice repeated in his mind. Outwardly his eyes fluttered, blinking the thought back.

"I am Morpheus," the man in chair spoke and moved a hand toward the woman, "This is Trinity, and this, as you already know, is Neo."

He looked at each of the three, trying to figure out these strange people with an apparent obsession with vinyl and sunglasses. "John Smith," he replied.

"That's not your real name," Trinity said bluntly. John shot her a look but he couldn't deny that he somehow agreed with her.

"Alright," he snapped, "Then what is it?"

"You tell us," said Neo. John was about to protest the absurdity of this conversation, but he stopped himself and thought about the voice in the dreams. What was it she called him? His frustration grew when he couldn't remember.

"You know what?" John said in a tone that clearly exhibited his aggravation, "I want to know what's going on here and who you people are aside from cop killers?"

"That cop was dead as soon as the agent took him over," Morpheus answered smoothly.

"Took over?" he shook his head and held up his hands in exasperation, "Look. Just start from the beginning and tell me what the hell you are talking about."

Morpheus smiled and rested his hands on the armrest as he leaned forward. "We are at war with the Machines. They grow human beings in factories and plug our minds into this," he motioned around him, "the Matrix. None of this is real. It is only a digital creation designed to keep mankind ignorant of their real purpose, batteries for the Machines."

Images of being submerged in the pink liquid flashed in John's mind causing him to flinch. He found what Morpheus said incredibly easy to believe. His interest peeked; he leaned closer and listened intently to Morpheus' monotone voice.

"Here in the Matrix, programs called Agents, control the populace by eliminating anyone who discovers the truth. One such agent, Agent Smith, was thought to be destroyed by Neo, but has instead become a virus slowly devouring the Matrix from the inside out."

"If what you say is true," John interjected, "Then isn't the virus a good thing?"

Morpheus shook his head, "Sadly, no. Each time he absorbs a person or program, he knows everything they know and they die."

"Is that what this, Agent Smith, was doing to me?" he asked Neo, who simply nodded once. "I don't understand. Why was he going through so much trouble to…absorb me?"

"Your presence here in the Matrix is a mystery, a mistake we're told," Morpheus answered, "you know something that can change everything and Agent Smith wants to know it too."

"But I don't know anything," John shook his head in denial, "I'm nobody. What does any of this have to do with me?"

"You are somebody. Someone important. You just have to remember."

John tried to think of what he knew that could be so important, but his thoughts were in such a jumble, he could barely think at all. "The Merovingian said that I was alien to the system," he thought aloud.

"Do you know about the blue box?" Morpheus asked. John jerked his attention to Morpheus and leaned forward. "The blue box?" he could not comprehend how they could know his dreams, "Police public call box. But that's from my dreams."

Morpheus and Trinity looked over to Neo, who took a step toward John and leaned over him. "This is a dream," Neo spoke in a calm voice, "you need to remember who you are. You need to wake up."

The words, wake up, resounded through his mind in that sweet, playful, worried woman's voice and he closed his eyes. _Wake up_, the voice said again, a voice he knew he was connected to, and he let it take hold of his thoughts. The flood gate opened and memories flowed through him like a river. The blue box. TARDIS with her doors open. A theft. The stars. A stream of time stretching billions of years. The fields of red grass. The golden citadel. A war. A scorched planet. Gallifrey. A little blue planet. Earth. Sarah Jane. Rose. Donna. Fighting. Saving. Crying. Loving. Laughing. Nine hundred years. Time Lord. The Oncoming Storm. The protector of Earth.

Oh yes, he remembered who he was and where he was. He remembered everything. The Doctor opened his eyes and stared a moment at the waiting faces of Neo, Morpheus and Trinity. With a slight tilt of his head, he offered a cheeky smile and said, "Hello, I'm the Doctor."

.

.

Programs across the city became aware of the new code in the Matrix similar to when Neo accepted that he was the One. Agent Smith, the virus, became aware as well and wanted this new power he could almost taste it. Moving as one, the Smiths all over the city moved to converge on one location.

.

.

Morpheus rose out of the chair. "An apple a day keeps the doctor away," he said smiling to himself that he discovered the hidden meaning of the Oracle's little riddle.

The Doctor raised an eyebrow, however, "Sorry. Come again?"

"A riddle from the Oracle," he answered with a dismissing shake of his head, "Her way of leading us to you."

"Oh, I see. A bit of clever. I like clever," the Doctor winked, then switched to seriousness. "Right. This business with the machines," he jumped to his feet and took a deep breath that made him pause. "Hang on," he whispered and put his hand on his chest with a frown. He looked at the trio a moment, and then closed his eyes in concentration. A faint golden light shimmered over his body.

Trinity seemed alarmed at first, but relaxed when Neo held up his hand to her and shook his head. When the glowing faded, the Doctor opened his eyes and smiled wide. "That's better!" he exclaimed as he rubbed his chest, "Two hearts. Two respiratory systems. Everything where it should be. I know this is just a digital rendering, but if I'm going to be me, it should be all the way, right?" He looked at the slightly frowning faces of Neo, Morpheus and Trinity, and his own smile faltered.

"Who are you?" Neo asked sternly.

"I already said, I'm the Doctor, but I think you actually mean _what_," he looked between the three, noting they didn't pry him for a name probably because they had their own monikers, he liked that. He nodded once at their silence. "The Merovingian was right. I am alien, or rather, _an_ alien to be precise. As in, not of this earth. You see, I am a Time Lord from the planet Gallifrey, and that blue box, oh that wonderful, beautiful blue police box, is my space ship. You found her in the tunnel, didn't you?"

"Yes, we did," Trinity spoke, "and we took it to Zion."

"She's ok, I hope," the Doctor asked, but frowned when Trinity didn't immediately answer.

"Doctor," Morpheus spoke and drew the Time Lord's attention from Trinity, "This is fascinating and quite unexpected, but you must _know_ something of great importance."

"Aside from everything in time and space," he smiled smugly and shoved his hands in his pockets, "I imagine the fact that the Source is also an alien could be considered something important. Don't think its too happy I know its little secret." The Doctor tried not to let it show he found the expressions of Morpheus and Trinity amusing, and chose to look even cleverer instead.

"If the Source is an alien," Neo seemed unfazed by the otherworldly topic, "is that why you're here?"

"Well, sort of," the Doctor rocked on his heels looking a bit embarrassed, "I didn't know anything about it until the TARDIS…uh, that's the name of my ship, landed me here. She has a mind of her own sometimes, and I _did_ set her to random."

"So you're not here to help us?" Trinity rightfully sounded upset.

"Oh, that's where you're wrong," the Time Lord said with a dark look, "I intend on ending this and making the Source pay for its actions against this planet. What the Source has done not only violates galactic law, but infuriates me to the core of my being. Not really looking good for the Source angering _me_, of all creatures in the universe."

"How did you come to be in the Matrix?" asked Morpheus.

"Greed," the Doctor answered flatly, "though lucky for me, I suppose. The Source could have killed me outright, but instead plugged me into a power plant because my Time Lord body apparently produces one hundred times the energy of a human. Mainly though, it didn't want me running off to the Shadow Proclamation."

"The Shadow Proclamation?" asked Neo.

"The police force of the universe. Only the Source doesn't have to worry about them. Just me," the Doctor said with malice in his tone before switching back to his normal voice and continuing. "Now, I need to find out what species the Source is so I know what I'm dealing with. Oh, have to find out how the time stream was changed. I've been to this century before and it wasn't overrun by machines. Did I mention I'm also a time traveler?"

Morpheus and Trinity shook their heads, but seemed to take the news in stride. "You mean none of this was supposed to happen?" Trinity asked with an understandable amount of anger creeping into her voice.

"Nope," answered the Doctor, "Don't worry, I can fix that, but I need to get out of the Matrix. I'll be more useful as the really real me.

"We can help you escape of the Matrix," Neo said, remaining stoic as usual, and reached into his coat pocket.

"Neo!" one of the men standing guard at the door ran up to him in controlled urgency, "Agent Smiths!"

Neo grabbed the Doctor's hand and smacked a red pill into his palm. "I'll see you in the real world," he said and stalked toward the steel door.

"Hang on to that," Trinity told the Doctor as he held the pill up to the light between a finger and thumb. "It's not safe for you to exit here. Follow me!" she said and ran with Morpheus toward what the Doctor assumed was a back door. He dropped the pill in a jacket pocket and quickly followed with a broad smile. Now, this was more like it. Knowing who he was, being chased by bad guys and running for his life. Ah, adventure.

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><p><strong>AN: the action continues in the next chapter :)**


	7. Chapter 7

**A/N: thanks for the review, Lordheaven :)**

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><p>Trinity burst through the rear door of the warehouse with a loud bang. Morpheus followed close behind her as he called Link for a new exit point. The Doctor came a few steps after. His need to turn and look when the interior brick wall exploded revealing an Agent Smith in the dust cloud cost him a couple precious seconds.<p>

Four sleek motorcycles waited for them in the alley. Trinity shed her vinyl overcoat, tossing tossed it to the ground as she mounted a motorcycle and motioned for the Doctor to ride with her. "Hope you like motorcycles," she said and fired up the bike's engine. The Doctor hopped on the bike behind her and wrapped his arms around her waist. "Sure!" he grinned, "I have a scooter." Trinity just shook her head with a sigh then asked Morpheus, sitting on his own motorcycle beside her, for the location of the exit point.

"Fifth and Seneca," Morpheus answered.

"That's far," she said with concern and pursed her lips.

"Well, what are we sitting around here for?" the Doctor said with the excitement of boy on a carnival ride, "Allons-y!"

.

.

The motorcycles roared as they sped down of the alley. Behind them, Agent Smith blew the door of the warehouse off its hinges sending it slamming into the building across the way. He stepped into the alley in time to see his quarry disappear around the corner onto the street. Before he could take a step, Neo slammed into him at full speed that sent him crashing helplessly through the building.

Without wasting any time, Neo launched himself into the sky and flew after the motorcycles.

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.

As Morpheus, Trinity and the Doctor sped down the street weaving around cars and completely ignoring traffic signals, the Time Lord was having a blast. The wide grin on his face hadn't faltered, though he did wish he had his glasses to help keep the wind out his eyes. To his surprise, his dark framed glasses suddenly appeared on his face. He thought about this and deduced that since he was now aware of the Matrix and himself, he could control it like Neo could.

As a test, he envisioned himself on the motorcycle with his tan overcoat flowing behind him like a cape. He looked down and sure enough, he was now wearing the coat. With an ecstatic laugh, he shouted, "Brilliant!" Trinity, who was focused intently on driving the motorcycle, called out to him over her shoulder. "I'll show you later," he beamed.

Behind the motorcyclists there was a cringe worthy crunch that drew the Doctor's attention. He looked behind and watched a crumpled car fly at an impossible speed toward them. It was going to hit them, he judged from its trajectory. He swallowed, unsure what to do, when the car suddenly stopped in mid-air. An airborne Neo swung it around and slammed it into a pursuing Agent Smith, knocking the virus into the pavement. A dozen more Smiths jumped into a pile on top of Neo dragging him down to the ground.

Trinity yelped and swerved the bike hard. The Doctor whipped his head around in time to see an Agent Smith standing in front of them. Trinity tried to earn some distance from the agent, but it wasn't enough. Agent Smith managed to grab the Doctor by his collar and yank him off the bike. To the Doctor, he felt like he hit a brick wall and even felt his body suspended in mid-air a long moment before getting slammed hard into the pavement.

The Time Lord lay on his back in a small crater, pinned to the ground under the incredible strength of Agent Smith's hand wrapped his neck. "We meet again, Mr. Smith," the agent growled with a dark smile and slowly lifted the Doctor up to his feet. The virus flattened his free hand and pulled it back.

"Sorry," the Doctor smiled tauntingly, "No Smith here, just the Doctor." He thought about how this person was not a person, but a computer program, and that his sonic screwdriver could scramble that program. The agent paused long enough for the Doctor to feel the sonic appear in his hand and activate it.

Agent Smith's face contorted in pain, and he howled in fury. He released the Doctor and doubled over as his code scattered back into the Matrix. The poor woman standing in Agent Smith's place closed her eyes and collapsed to the ground. The Doctor lunged forward and caught her in his arms. Gently, he lowered the woman to the ground and checked her vitals. He knew she was dead before doing that, but he held out hope that what Morpheus said about the take over wasn't true.

He frowned with sadness as he looked at the dead woman's face. "I'm sorry," he whispered. A motorcycle roared up beside him, and he looked up to see Trinity. "Are you alright?" she asked. He nodded and looked toward Neo with a clenched jaw. The One stood in the middle of dozens of Agent Smiths, punching, kicking, and killing them like they were meaningless playthings. The Doctor felt his rage well up inside him at the thought that each of those agents is an innocent human being.

Of course, he knew Neo knew this, but to Neo and his allies, this was war and these people were unfortunate causalities of that war. However, it wasn't Neo's fault. He and the others were driven to this in a desperate attempt to stay alive, to survive. And it was all because of some alien that was only interested in harvesting energy for itself. He climbed back onto the motorcycle with Trinity. "Let's get to that exit point," he said.

.

.

A few minutes later, they arrived at the exit point, a simple public phone booth on a not so busy side street in downtown. Neo was able to clear the path of Agent Smith's and the virus eventually ceased his attacks. Trinity parked the motorcycle, and the Doctor climbed off the bike. His spiky hair stood on end and he looked liked he'd just had the best experience of his life. "I'd say let's do that again," he grinned, then turned serious, "but there's lives at stake."

Morpheus dismounted his bike and stood in front of the Doctor. "You weren't wearing the coat when we left the warehouse," Morpheus asked in a tone of cool observation.

"Yes, well," he put a hand on the back of his head and raised his eyebrows, "it seems I can make things appear when I need them."

"That could prove very useful," said Morpheus.

"It is rather brilliant, isn't it?" grinned the Doctor, "but I'll be much more useful in the real word."

"What did you do that agent?" Trinity asked as she slid off the bike.

"I thought of him as what he really is, computer code," the Time Lord answered casually, "my sonic screwdriver can scramble code and when it materialized in my hand, I used it. So, where's the exit?"

Morpheus motioned to the phone booth. The Time Lord couldn't contain his amusement. "Noooo, really? Oh, that's lovely," he laughed as he walked up to the phone booth. "I just can't seem to get away from phone boxes. And this one's even blue! How does it work?"

"For us," Morpheus indicated himself and Trinity, "it's a simple phone call, but you must swallow the red pill."

The Doctor dug into his pocket and held up the red pill to the sonic. "What does it do?" he asked looking at the pill with curiosity when the sonic didn't tell him anything.

"It's a script that disconnects you from the Matrix," Morpheus explained, "You will awaken in the power plant, and you will be flushed, but the script embeds a signal in your implants that we can trace."

The Doctor nodded slowly as he processed the information and mentally examined possibilities. "Implants," he smiled brightly with realization. "Of course!" he exclaimed snapping his fingers, "That's why my integration into the Matrix failed. I never really had a chance to think about it until now, but ooohh what a mistake the Source has made with me!"

"What do you mean?" asked Trinity.

"Being the Time Lord that I am," he held up a pointing finger, "my body just can't do with implants and is really good at rejecting the lot of em. I imagine the machines have been rather busy keeping them in place. That would explain the dreams I had of being in that pod…I was really waking up! Tell me you can take the implants out?'

"When we have you on board our ship," Morpheus said with reassurance, "we'll be able to remove all of them except the one in your head."

"You have to remove that one too," said the Doctor in all seriousness.

"We can't," Trinity said, "but Neo is coming and we have to go."

The Doctor grabbed Trinity by the shoulders and looked her in eye, "Listen to me, Trinity. You _must_ remove _all_ the implants, or I will be stuck in a healing coma until you do." He paused and held his hard gaze until she nodded.

He let her shoulders go and took a step back just as Neo landed a few feet away. He quickly strode over to the trio and said, "I've cleared the area, but it won't stay safe for long." He looked at the Doctor, "You must swallow the red pill now. I will stay here until everyone is out."

With a deep breath, the Time Lord looked at the red pill in his hand. He hated taking pills, but at least this one wasn't a real one. He looked between Neo, Trinity and Morpheus, "I'll probably be in that coma when you find me, and it may even look like I'm dead, but take out all the implants and I'll be fine. Try not to let me lose too much blood. I'm the only Time Lord left so you won't be able to ask for a transfusion."

The three nodded and Neo rested his hand on the Doctor's shoulder. "Don't worry, Doctor," he said, "we'll take care of you."

With a deep breath, the Time Lord lifted the pill to his mouth and paused. "I almost forgot," he raised an eyebrow and reiterated his words with his hand, "do not, under any circumstances, give me any pain killers, especially of all things aspirin. It'll be the death of me. Got it?"

"Completely," Neo said evenly and Trinity nodded.

"Alight," he said. He dreaded taking the pill, but he knew he had too. With a shrug of his shoulder, he popped the red pill in his mouth and looked at Neo with a cheeky smile. "Allons-y," he said casually with a hint of excitement and swallowed.

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><p><strong>Next chapter, back to the real world!<strong>


	8. Chapter 8

**A/N: Truwq, thanks for the review!**

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><p>When the Doctor opened his eyes, his first instinct was to panic, but he controlled the urge. He blinked at the feel of the liquid on his eyes and he knew he didn't have long to stay conscious. He was shocked out of the healing coma, but it was already starting to take hold again.<p>

Still, he managed to sit up half way out of the liquid and once he was upright, he pulled the hose out of his throat. Feeling that hose slide through his respiratory system made him gag and cough, but once he was able to breath, he got a good look of his surroundings. To say that he felt horrified at the sight of the entire human race trapped in pods would be an understatement. He was furious and couldn't wait to get his hands on the wretched alien responsible.

Suddenly, a robot, like the one that put him in the pod in the first place, appeared and grabbed him by the head with a metallic claw. It pulled him up and he struggled helplessly against the mechanical arm. The robot went about its program and attached a device to the plug on the back of the Doctor's head. With a brief drill sound, the machine yanked the cable free, released its hold on the Time Lord and flew away to tend another pod.

He fell back into the thick liquid with a splash and instinctively touched the back of his head. He felt sick at the feel of the socket back there and looked forward to it being gone. One by one the hoses connected to the implants across his body popped off, each one sending jolts of electricity that made him grit his teeth in pain.

The Doctor barely had time to recover when the system flushed him feet first down a tube. As he sped down the tube, he recollected the time he and Ramona went to one of the largest water parks in the universe on beautiful Rigel Seven. There wasn't even anything dangerous happening at the time, it was just good fun. He smiled at the memory as he struggled to stay awake.

Just when he was about to succumb to the coma, the tube ended and he shot out into the air. Flailing helplessly, he landed with a splash in a pit of waste water. The impact woke him a little more as he fought for the surface and took a desperate breath of air when he reached it. He looked around for a place to climb out of the muck, but there was nothing but smooth, steep walls as far as he could see.

He treaded water and it was taking all the energy he had left to keep his head above the surface. He hoped Neo and the others would find him soon because he wouldn't be able to keep this up for long.

.

.

"Hurry, Link," Trinity said with desperation in her voice.

"Almost there, and…there!" the operator said with a smile.

She rushed to the back and watched as Neo and Morpheus dropped the claw into the waste water below. After a few moments, the claw reappeared with the limp body of the Doctor in its clutches. They quickly brought him aboard the Nebuchadnezzar and into the infirmary. There, Trinity gave the Time Lord's naked body a swift wipe down around the implants to clean the way for surgery to remove them.

"He isn't breathing," she said and pumped on his chest to resuscitate him. Morpheus attached the monitor and frowned. "One heart beat," he stated in an observational tone. Trinity ignored him, opened the Doctor's throat and breathed air into him. She pumped his chest again. This time he convulsed and choked up water, but after a couple of violent coughs, he lay still. The heart monitor now beeped for two hearts and Morpheus simply looked down at the Doctor with curiosity.

Now that the Doctor was breathing, as shallow as it was, Trinity assumed this was the healing coma he told her about. His skin was cold, too cold, and dark rings formed around his eyes almost like he was dead. But he warned her about that too, so she set to work on removing the implants. When she removed the first one, orange-red blood seeped out of the wound. "Look at this," she said before she covered it with a cloth bandage.

She looked at Morpheus and Neo with a bit of surprise at the color of the blood, but continued until the only implant left was on the back of his head. Neo gently touched her hand to stop her, "Are you sure you need to do that?" he asked.

Trinity looked at him, concern embedded on her face. "He told me too," she swallowed with nervous determination, "he said that if I didn't, he would never wake up."

"Trinity," Morpheus spoke in an even tone, "do it."

Neo moved his hand and stepped back to give her room. She looked between the two men for support, who gave it with a grim nod, and then focused on the Matrix access plug. With a deep breath, she attached a pair of forceps to the implant and started pulling it apart.

.

.

The Doctor opened his eyes and looked into the large brown eyes of a little girl. He smiled. "Hello, there," he barely managed to whisper. She smiled in return, and then ran away into another room. He lay on his side on a hard mattress in a bedroom with walls carved in stone. The air had an earthy aroma underneath the flavors of cooking food, but most importantly, he could smell that he was in the twenty-second century.

The smell of food caused his stomach to rumble letting him know that it was empty. He was also very thirsty; it hurt to swallow against his parched throat. Slowly, he swung his legs over the edge of the bed and sat up. He held out his arms and looked them over, noticing that he was clothed in a drab gray sweater with frayed edges and simple brown pants. He pulled back a sleeve and frowned at the bandages wrapped around his forearm. Curious to see how the wound from the implants had healed, he removed the bandage and was quite pleased. Barely a mark at all.

Then he remembered that plug in the back of his head and instinctively touched the area with his fingers only to find that his head was wrapped in bandages as well. His fingers sought out the end of the wrap and just when he found it, a woman entered the room carrying a bowl and a cup.

"Hello, Doctor," she said in a warm voice and friendly smile, "I'm Zee, Link's wife. How are you feeling?"

"Allo Zee, I'm…" the Doctor's voice cracked causing him to cough uncontrollably.

Zee offered him the cup filled with clean water that he quickly emptied. The water helped immensely. Clearing his throat, he said, "Thank you." He noticed the little girl was hiding behind Zee's legs, so he smiled and offered a little wave. The girl smiled shyly.

"Of course," Zee said, "You must be hungry. Here," she handed him the bowl, "I'll be right back with some more water."

The Doctor nodded as Zee and the child left the room. He sat holding the bowl full of what looked to be porridge. Trying a bite, he decided he wasn't that hungry and could probably hold out until he got to the kitchen in the TARDIS. He sat the porridge down on a small handcrafted table next to the bed, noting a pair of dingy black boots on the floor next to it, and worked on removing the bandages from his arms.

Zee came back in the room with a full cup of water. "You seem to be healing up just fine," she noted his uncovered arm, "I was told of your…unique ability."

The Time Lord smiled in response and took a drink. "One of my many talents, I assure you," he sounded a bit smug, "How long have I been here?"

"Since yesterday," the woman replied, "I'm honestly surprised to see you awake so soon. Trinity removed the plug from your head, but she was concerned you wouldn't make it."

"Oh, it'll take a bit more than that to take me down," he gave a cheeky smile, "Where is she?"

"I told her and Neo you were awake. They should be here any minute. If you'll excuse me, I have to check on dinner," she turned to walk away, "holler if you need anything."

"Thank you, Zee," he called after her as she left the room.

He felt anxious to get the bandages off his head and quickly unwound the cloth. In a few seconds, the strips draped across the bed and he peeled away a thick bandage. He looked at his blood dried on the bandage for a moment before tossing it aside. Running his fingers through his hair, he smiled. No plug. No wound. He was good as new.

He heard Zee in the other room welcoming Trinity and Neo, and the pair appeared in the doorway of his room after a few moments. "Glad to see your up, Doctor," Trinity said and walked over to him, while Neo leaned against the doorframe with crossed arms.

"Good as new thanks to you," he smiled brightly, "You were brilliant."

She smiled slightly at the compliment as she leaned over to see the back of his head and was surprised to find no trace of the plug that she pulled out the day before. "You're completely healed," she said, the surprise lingered in her voice.

"Yes indeed," he stood up and stretched, "Ready to take on the Source, but first, I would love to see my ship."

"It's at the Dock," Neo said evenly, "I'll take you there."

.

.

The Doctor was amazed at the city, Zion, these humans carved out for themselves. Its structure spoke of ingenuity, but also desperation. Still, the city reminded the Time Lord why he loved humans so much and that now more than ever they needed his help.

Finally, the corridor Neo and Trinity led him down opened up into an immense cavern that held him in awe as he stared at the large portals in the far walls for ships and the expansive platform that seemed to cover the entire circumference of the cavern. Neo pointed over to the right toward a hovercraft, and the Doctor's eyes fell on his beloved blue box.

He was overwhelmed with happiness at the sight of the TARDIS and almost shed tears of joy as he ran over to the time ship. The wave of emotion puzzled him briefly until he remembered his dreams in the Matrix. It was her calling out to him; it was her that saved him. He ran the palm of his hand lovingly over the wood panel door and snapped his fingers.

Neo and Trinity caught up to the Doctor as the TARDIS door opened and he bolted inside. Neither of them could believe their eyes at the sight of the console room. "Ooohhh look at you, old girl!" the Doctor exclaimed running his hands over the controls just like he did the first time he touched them. He beamed an ecstatic look over to Neo and Trinity lingering in the doorway.

"Come in, come in," he waved excitedly and then spread his arms out, "This is the TARDIS, my space ship and time machine! Isn't she beautiful?"

Trinity nodded and even Neo's expression showed his appreciation. "It's so much bigger in here then the outside," Trinity said as her eyes drifted over the coral support beams.

"That never gets old. Dimensionally transcendental rooms," the Doctor happily explained with pride, "and this ship can go anywhere and any when. This is how I'm getting to the Source, I just need the coordinates."

"Leave that to me," Neo said with conviction.

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><p><strong>AN: thanks for reading so far and as always your reviews are really, really awesome :D  
><strong>


	9. Chapter 9

**A/N: Lordheaven, thanks for the kind words (you rock), and I'm happy you like the allons-y's. :D :D  
><strong>

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><p>"I'll let Morpheus know we're heading back up," Neo said and promptly left the TARDIS without another word.<p>

The Doctor watched him go and glanced at Trinity. "He seems like he has a lot on his mind," he said to her.

"Yes. He is the One," she sighed, "and that means the fate of Zion rests on his shoulders."

"Good thing I'm here to help then, isn't it?" he gave her a wink.

She looked at him and smiled, "I really hope you can."

The Doctor offered a reassuring smile as he looked down at the console and for the first time, noticed the floor. "Oiy, what happened in here?" he puzzled over the articles of clothing and other belongings scattered throughout the room. He picked up a shirt and dashed over to the monitor. He flipped a couple of switches and his eyes grew wide at the recorded video playing before his eyes.

"You shot my ship?" he asked in disbelief.

Trinity approached the console and looked at the monitor. "It was Commander Lock," Trinity explained with a sigh and a shake of her head, "Councilor Hamann tried to stop him."

The Doctor dashed out the TARDIS door and gawked at the few bullet holes that not only managed to dint the ship's sturdy exterior, but completely escaped his notice in his happiness of being reunited with his ship. "Why would anyone want to shoot a blue box?" he didn't hide his disbelief or anger.

"Because it could be dangerous," boomed a deep voice in response.

The Doctor spun around to face the source of the voice and glared at a stocky, muscular man wearing a dark scowl walking up to him with an air of authority. He was followed by an older man in a flowing robe wearing an apologetic expression. The Doctor easily guessed which Commander Lock was, and stalked up to the man until he stood inches away.

"Dangerous?" the Doctor spat.

"We've never seen anything like it and for all I knew, it could have been a weapon from the Machines," the commander held his ground and stared the Doctor down, "still could be as far as I'm concerned."

"Does that," the angry Time Lord pointed back at the TARDIS, "look like anything from those Machines? Okay, so you don't know what it is, so you just decide to destroy it? Are you daft?"

"My duty is to protect this city," Lock bristled, "and you're an alien. I should have you locked in the hold until I can determine whether you're a threat or not!"

The Doctor slapped his hand on top of his head in astonishment. "Daft _and_ an idiot! Well, what are you waiting for?" he challenged, but the elderly man stepped between the Doctor and the commander gently pushing them apart.

"Gentlemen, please," he said in a calm voice, but he shot the commander a disapproving glare. Facing the Doctor, he wore a friendly smile and said, "Please forgive Commander Lock here, he's just a bit overzealous of his duty. I have been assured that you are no threat. I'm Councilor Hamann." He offered the Doctor his hand.

"Overzeal…" Lock started, but the councilor silenced him with a glare over his shoulder.

The Doctor looked over the councilor and shook his hand. "I'm the Doctor," he said in a calmer tone, but he was clearly still upset.

"Neo has told me everything about you, Doctor," Hamann said and strategically walked the Doctor away from Lock and toward the TARDIS, "and I must say, you are a very fascinating individual."

"I suppose you can say that," the Doctor cracked a smile.

"An alien," the councilor continued, "I never would have imagined, and you say that the Source is also an alien?"

"Yes it is. Though I don't know what species yet," the Time Lord stopped at the doorway of the TARDIS and nodded to Trinity when she walked past him toward the Nebuchadnezzar. "Whatever it is, it must have crashed here at some point and created all of this."

"Are you sure you can stop this alien?" asked Hamann with concern in his voice.

The Doctor beamed his usual air of confidence, "I'll figure out something. Don't you worry. I usually do."

"I hope you do," the elderly man smiled. "Oh, I almost forgot," he reached into a pocket in his robe and produced a silver cylindrical object. He presented it to the Doctor, "Am I to assume this belongs to you?"

"My sonic screwdriver!" the Time Lord exclaimed brightly.

"That is quite the weapon," the councilor said as he handed it over with a warm smile.

"Oh it's not a weapon," the Doctor corrected, "but it is the most useful tool ever to exist in the universe. Thank you." He went to tuck the sonic into his jacket pocket but realized he was still wearing the sweater and pants, so he just held it in his hand.

"Well, that's some tool," Hamann replied, "It stopped a mech cold."

"Oh yes. It's perfect for shutting down machines. Care for a tour of the TARDIS?" he placed a foot over the threshold of the TARDIS and smiled wide when the councilor nodded his head. He stepped aside to let Hamann in then shot a look at Commander Lock who was watching him with a dark glare. "You're not invited," he said in a stern voice. The commander clenched his jaw and stalked away. With a smile of victory, the Doctor entered the TARDIS and happily talked to the councilor about his ship.

.

.

The hour that followed was a busy one. The councilor was quite curious about the nature of aliens and the universe, which the Doctor recognized the man was assessing him as a threat in his own way, but when Hamann finally left to attend other business, he seemed satisfied that they were both on the same side.

Morpheus paid a visit to discuss a plan of attack and didn't stay long at all. Once he was left alone, the Doctor picked up as much of the clothes and items from the floor as he could in one pass and made a mental note to see why the internal stabilizers weren't working. In the Wardrobe room, he cleaned himself up and changed into his blue suit and red trainers. He stopped by the kitchen for some sweet bread and of course, bananas, stuffing a few extra into his jacket pockets. When Trinity came to inform him they were ready to load the TARDIS onto the Nebuchadnezzar, he swallowed the last of a banana, shoved the peel down a clear tube in the console, and gave her a wide smile as he left his ship.

A loading mech was waiting outside the TARDIS and the Doctor made it clear to handle the blue box carefully. While the mech walked the time ship into the Nebuchadnezzar, a large group of people had gathered on the Dock. Many of them brought gifts and praise for Neo, while some regarded the Doctor with curiosity, but kept their distance. That didn't last long however, the Time Lord happily introduced himself with a friendly smile and shake of the hand. Soon, he was answering questions about his clothes, planets, aliens and food.

Finally, Morpheus announced they were ready to depart. The Doctor said his good-byes to the good people of Zion and saw Zee walking slowly to the hovercraft holding hands with a man holding her little girl. He must be Link, the Doctor reasoned and approached the family. Zee smiled her warm smile and introduced the Doctor to her husband, who seemed thrilled to meet the now conscious Time Lord.

"Are you really an alien?" Link's daughter suddenly blurted out.

"Why yes I am," the Doctor smiled, "Don't believe it?"

She shook her head.

"Would it help if I did something no one else can do?"

She nodded.

"Alright. Look at this," the Doctor lifted the corner of his jacket and demonstrated that it was flat, "Couldn't be anything in there, right?" The girl shook her head, but watched with wide, fascinated eyes as the Time Lord reached into the pocket and produced a banana.

The girl's face light up with surprise as she stared at the yellow fruit with curiosity in her eyes. The Doctor peeled the banana and handed the fruit to the girl, who took it in her hands carefully. "Take a bite, you'll love it," he said and she took a small bite.

Her expression made the three adults laugh. "Do you think I'm an alien now?" the Doctor asked her. She nodded vigorously and took another, much larger bite of the banana.

"Here," the Time Lord turned to Zee and gave her a banana, "I have one for you too. Thanks for taking care of me."

She took the fruit with a pleased smile, "My pleasure, Doctor."

"We should get going," Link said as he sat his daughter down and gave his wife a kiss.

"Yes, time to get down to business," the Doctor replied.

.

.

Once Link landed the Nebuchadnezzar in the tunnel, Neo climbed into the chair and prepared to jack in to the Matrix. When Trinity climbed into the chair next to him, he protested and started an argument that Trinity eventually won. The Doctor stood aside, leaning against a wall out of the way, and watched the pair settle into their chairs. He joined Morpheus and Link in wishing them luck. Morpheus plugged Neo in first, then Trinity, and their bodies fell limp.

Morpheus took a position behind Link and watched the monitors stream the green falling code of the Matrix. The Doctor moved to stand next to Morpheus and after a silent moment of staring at the monitors, he asked with curiosity, "Can you really tell what's happening?"

Link chuckled, "Yes. Understanding the stuff takes some practice though."

"Why don't you just display a video?"

"Can't," replied Link, "the Matrix is too vast for these old computers to handle. Lucky we can see this."

"Well, let's just see about that shall we?" the Doctor grinned and held up his sonic screwdriver. After slipping on his glasses, he knelt in front of the console next to Link's chair and waved the sonic over the computer components a few moments, then stood and touched the sonic to a monitor. The screen flickered but when the Doctor slapped the side of it, the display showed Trinity riding a motorcycle down a street.

"Hah!" the Doctor exclaimed proudly with a cheeky smile.

"How did you…" Link was flabbergasted. Morpheus simply uncrossed his arms and gave the Doctor an incredulous look.

"Simple," the Time Lord said smugly, but shrugged his shoulder like what he did really wasn't a big deal, "I overclocked the main processors as high as they would go, fine tuned the rapid access memory to its maximum and amplified the video hardware. In short, I gave it an upgrade. Oh! Let's get Neo." He waved the sonic over another monitor and it instantly displayed Neo walking through a park approaching an older woman sitting on a bench. "There," the Time Lord said, "like watching a movie."

"That's amazing," said Link, his eyes fixed on the monitors.

"Thank you," the Doctor beamed. He just loved feeling appreciated.

The room fell silent as the three watched Neo hold his own in an incredible battle with countless Agent Smith's in the park. Finally, Neo took to the air and left the Agent's behind. Eventually, he landed in front of a door, and when he walked through it, the monitor went blank white.

"He found a back door," Morpheus said evenly, "We won't be able to see him while he's in there."

"Uh oh," said Link in a grave tone, "we've got trouble. Sentinels."

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><p><strong>AN: now, I am not computer hardware person but I understand the basics, so I hope the Doctor's explanation to Link is ok. If not, let me know as I'm not opposed to changing it. Either way, I'd love to know what you think of the story so far. Thanks!**


	10. Chapter 10

**A/N: No more slow chapters, I promise you, well except for maybe the ending. But for now...back to the action!**

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><p>The holographic display depicted the squid machines flying on an intercept course with the Nebuchadnezzar. Both Link and the Doctor watched the holograms with a grim expression.<p>

"How many?" Morpheus asked Link.

"Twenty. At least."

"How much time do we have?"

"They're going to be on us in less than ten minutes," the operator swallowed.

Morpheus looked at Trinity and Neo currently jacked in to the Matrix and clenched his jaw. He looked back to the monitors. Neo's screen was still blank, and Trinity was evading a couple of Matrix agents. "We need more time," Morpheus said.

"Surely you have a weapon against the robots?" the Doctor asked.

"We do, but it's an EMP," Link answered and nodded toward Trinity and Neo, "we can't use it while their plugged in to the Matrix."

"Electro-magnetic pulse," the Time Lord thought about this and then lit up with an idea, "the machines don't like sonic waves either. If I can modify it to a sonic pulse that only affects the sentinels…"

"You'll be able to use it while their jacked in!" finished Link with a grin.

"Yes!" the excited Doctor said, "Show me where that EMP generator is."

Morpheus motioned for the Doctor to follow him, and led the Time Lord into the section of the hovercraft that housed the generator. The old machine looked larger than the size it really was tucked into the small room surrounded by hoses and pipes. The Doctor could tell at first look that the engine was pieced together with random parts held together by greased bolts and pure human will.

The point of interest for the Doctor was the simple control panel on the side the generator that had one row of three buttons labeled on, off, charge, and ready. The on and charge buttons glowed with a dim green lit. After a quickly examining the panel with the sonic, the Doctor removed the screws of the panel face.

He pulled the panel down to reveal a set of wires leading from the buttons to somewhere inside the generator. Shoving the glasses that slid down his nose back up, he tracked where the wires routed through the machine, then reached in and yanked out a large cable. He paused a brief moment frowning at the black grease spot on the sleeve of his clean blue suit, but continued to pull out the cable until he found what he was looking for, a plug connecting the two cables together.

With the sonic in his mouth, he unplugged the cables and tossed one aside. Then he held the sonic to the end he still held in his hand and activated the device.

A spark popped out of the generator, but the Doctor was not alarmed and instead smiled with success. "Sonic pulse is now online! Tell Link to fire when ready," he said to Morpheus who pushed a button on a small panel by the door and relayed the message. The operator reported that the sentinels were within range and Morpheus gave the order. The generator's soft hum escalated into a very audible whirring squeal as the machine shoved the sonic pulse out toward the sentinels.

"Woo hoo!" shouted Link over the com speakers, "That took em down!"

Morpheus grinned and patted the Doctor on the back, "Good work, Doctor." The Time Lord laughed, always enjoying the feeling he got when his plans worked. The celebration was short lived however, as sparks popped from the old machine. The Doctor snatched the sonic off the plug, but it was too late. With a loud bang, a puff of black smoke rolled out and the generator shuddered to silence.

"Oh no!" the Doctor cried as he rushed over to the wires and frantically picked over them.

"Did the sonic pulse overload it?" asked Morpheus as he too, looked over the generator.

"I'm afraid so," sighed the Time Lord, "it must have been too much for this old thing to handle."

"Maybe we can get it running again and just use the EMP," Morpheus stated in an even tone that made it difficult to tell if he was upset or not. The Doctor wondered if any human could be more stoic. Then he thought of Neo and stood corrected.

"Yes," he agreed, "let's try that."

With Morpheus' help, the Doctor had the generator pieced back together in no time. Morpheus had just restarted the machine when Link's voice sounded over the com, "We have more sentinels. Lots of em." The fear in the pilot's voice struck a tinge of panic in the Doctor's hearts and looked at Morpheus wearing a hardened grim expression.

"Stay here and make sure the generator stays running," ordered Morpheus, "I'm going to see if Neo and Trinity are ready to leave the Matrix."

The Doctor shrugged his shoulder. After all, he didn't have anything else to do at the moment.

.

.

He hated being in that room not knowing what was happening out there. Sure, it must have been only thirty seconds, but that was thirty seconds too long. The Doctor double checked the generator, it ran smoothly, maybe even better than before, and headed out of the room. He took a couple of steps in the corridor when he heard a metallic thud above him followed by the sound of a laser cutting into the hull.

The Doctor ran down the corridor and burst into the cockpit. He saw Trinity sitting up in her chair, she was out of the Matrix. But Neo was still unconscious, still in the Matrix. "The sentinels are on us!" Link shouted at Morpheus, "We have to do something!"

The situation was getting tense. The Doctor shoved his way to the monitor and watched Neo land at a telephone booth and picked up the handle. "Operator," Link spoke into his headset with a sigh of relief and tapped on the keyboard in front of him. Neo's image on the monitor dissolved into Matrix code and vanished into the phone.

In the chair, Neo gasped and opened his eyes. Without wasting any time, Trinity pulled the plug out of the back of his head. A part of the ceiling peeled away revealing a sentinel. The Doctor aimed his sonic at the machine and didn't let up until it fell unmoving to the floor. The lightning crack of an EMP rifle resounded through the room as the blast struck a second sentinel sending it crashing to the floor.

Suddenly, all the electrical in the ship shut off leaving the hovercraft in the dark for a moment. Then the humming of an EMP resonated through the hull of the hovercraft and the dark tunnel flashed with light. The Doctor tilted his head and listened intently to the thuds and bangs echoing on and around the ship.

"Falling sentinels," Trinity whispered.

"Get us out of here, Link," Morpheus said.

Link answered by restoring the power and flipping on the engines. The Doctor moved to Neo still sitting in the chair and before the Time Lord could say a word, Neo said, "I got the coordinates."

The Doctor smiled with pride, "You were brilliant, Neo! Absolutely brilliant," and offered him a hand out of the chair.

"Thanks," Neo took the offered hand and slid out of the chair.

"Oh my god," the pilot whispered in horror as he stared at the hundreds of sentinels on the scanner in the tunnel ahead of them and yanked on the ship's controls.

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Outside, the hovercraft flew down the tunnel and suddenly turned left into a smaller tunnel. The Nebuchadnezzar wasn't built for such tight turns and one of the side lift disks caught on the corner, ripping it off the hull. Sentinels by the hundreds streamed up to the corner and flowed after the hovercraft like a river of black ink. Unbeknownst to the crew of the Nebuchadnezzar, hundreds more sentinels lay in wait just a mile down the smaller tunnel. They were trapped.

Link deftly steered the hovercraft down the tight tunnel and allowed the adrenaline flow through his veins. He was just starting to feel a bit cocky at his truly excellent piloting skills when he rounded a bend and crashed the Nebuchadnezzar into a squirming wall of sentinels.

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"Hang on!" Link screamed and braced himself for impact as the Nebuchadnezzar dove nose first into the squid machines. The banging the metal bodies made as they struck the hull were nearly deafening, and the motion of the ship came to an abrupt halt as it smashed into the tunnel floor knocking everyone standing inside to the floor.

The Doctor, Morpheus, Neo and Trinity climbed to their feet and stared wide eyed at the incredible numbers of the sentinels flying right outside the cockpit window. When one sentinel landed over the window and activated its red laser beam to cut through the thick glass, the four took several instinctive steps back.

"Can you use the EMP again?" Trinity asked listening to the sounds of countless other sentinels landing on the hovercraft and using their cutting beams on the hull.

Link shook his head, "Not enough time to recharge."

"The TARDIS!" the Doctor shouted, "Come on!"

The Doctor sprinted out of the cockpit followed by Morpheus with an EMP rifle, Neo, Trinity and Link with a second EMP rifle. They almost made it to the cargo hold door when the roof opened up and sentinel dropped in. The Doctor disabled the machine with his sonic, while Morpheus turned down a side corridor leading the group down another route to the hold.

Sentinels were now crawling after them like spiders down the corridor. As soon as one was disabled by the Doctor or Link, another would take its place. Finally, the fleeing group burst through a hatch door into the cargo hold and Link slammed the door shut behind him.

The Doctor noted that the machines were cutting through the hull right above them and would break through any second, so he didn't waste any time running into the TARDIS. Trinity and Neo ran in to the time ship next, and the Doctor cringed at the sound of tearing metal in the Nebuchadnezzar's hull. He knew the sentinels had broken through. Morpheus and Link stepped inside the TARDIS and fired their rifles at the same time.

"Close the door!" the Doctor shouted and Morpheus slammed the wooden door shut. The Time Lord dashed around the console to the monitor and saw sentinels pour into the cargo hold. One machine was at the TARDIS door attempting to cut in with its laser. As he frantically pushed buttons and flicked switches, the image on his monitor was blacked out by the number of sentinels crawling over the blue police box.

The Doctor wasn't really worried about the machines breaking through the TARDIS' defenses, but he didn't want to stick around to give them the chance. He smiled wide at the sound of the time ship's engines whooshing to life and whisking them into the Time Vortex. He also enjoyed the mental image he had of the machines falling into a pile on themselves as the TARDIS vanished out from underneath them.

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><p><strong>AN: Keep the reviews coming, your thoughts are appreciated!**


	11. Chapter 11

After just a couple of seconds and a soft thud, the TARDIS' engines winded down to silence and the Doctor smiled. "Here we are," he beamed, "Zion."

Link, standing with the others at the console, was still trying to wrap his mind around the impossibility of the alien ship and the alien's announcement added to his astonishment.

"Thank you, Doctor," Morpheus, "we are in your debt."

The Time Lord crunched his face and waved at Morpheus, "No you're not, really. This is what I do all the time." He smiled a smile that showed he meant what he said and Morpheus nodded once. "Now, Neo, those coordinates, please." Neo gave the information and the Doctor programmed it into the TARDIS computer.

"Doctor, about the Source," Neo started and the Doctor looked him in the eye, "it wants to talk to me, in person."

"What?" the Doctor asked with a perplexed expression that Trinity shared.

"There is another enemy we have to deal with," Neo explained, "Agent Smith. He has absorbed over half the populace in the Matrix and he won't stop until he is the only thing that exists there."

"What does that have to do with the Source?" Trinity asked.

"It's obvious the Source is powerless to stop Agent Smith," the One looked at each of them, "I believe it wants me to stop him."

"Can you?" asked the Doctor.

"I'm not sure," Neo's self-doubt became evident on his face, "but if I defeat Agent Smith, I can reset the Matrix and save the lives of everyone he's absorbed. In return, I will ask for the machines to leave Zion alone. It should be an acceptable proposal."

"But, Neo, I _must_ find the alien behind this and stop it," the Doctor insisted.

"And you should, Doctor," Neo agreed, "Once the humans in the power plants are saved, find the alien and destroy it. End all this once and for all."

The Doctor understood Neo's plan and nodded. "I don't know about the destroying part, but one way or another, I will stop that alien and remove it from this planet."

"I need to find a ship. I don't think you should be the one to take me, Doctor," Neo said, "I don't want to alarm the Source." When the Doctor nodded once in agreement, Neo headed for the door.

Link and Trinity followed right behind Neo as he left the time ship, and the Doctor and Morpheus stood in the doorway a moment looking at the chaos on the loading dock. "The final battle has begun," Morpheus sighed with a knowing smile as if he'd been waiting for this moment a long time, and walked away.

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The Dock was a frenzy of soldiers heading to and fro, and mechs moving crates into position. The Doctor leaned in the door frame of the TARDIS watching the chaos and became aware of a rumbling sound steadily growing louder from the cavern ceiling above.

"Excuse me," he caught the attention of a young man running by and pointed up, "What's that rumbling noise?"

"The machines have been drilling through the earth to get to us," he said quickly with a grim expression, "they're really close so we're getting ready to fight." The Doctor nodded and the man ran off. The Time Lord sighed. He hated violence, even though it seemed to follow him like a bad plague. These machines and this alien presence was still a puzzle to him. He wondered how this all came to be right under his time-sensing nose.

He broke from his thoughts when he saw Neo and Trinity jog up to him. He smiled at the sight of the two, so in love, it was obvious. Trinity would follow Neo anywhere, no matter how dangerous. Just like Rose would follow him. How he missed her.

"Doctor," Trinity spoke, "we're taking the Logos to the surface. It shouldn't take us long."

"When the machines stop," Neo said, "go."

"I will," said the Doctor. He couldn't resist giving the both of them a hug that took the pair by surprise, "Be careful."

"You too," Trinity said and they both ran toward a hovercraft. The Doctor watched the craft lift off and disappear through an exit portal.

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Less than an hour later, the machines broke through the cavern ceiling and descended on the city of Zion like a storm. The Doctor teleported the TARDIS off the Dock and parked it as close to the back stone wall as possible to get it out of the way of the battle mechs and falling sentinels. He helped the women and children retreat to a safer location deep into the earth behind the city, and once they were sealed away, he made his way back to the Dock.

He stood for a moment at the archway he came out of and stared at the full scale war happening right before him. Battle mechs firing massive guns and the roar of thousands of sentinels flying around the cavern was deafening. When a dead sentinel landed with a crash right in front of him, he decided it was time he waited in the TARDIS.

Once at the console of his beloved time ship, he watched the action outside on the monitor. He was waiting, and he hated waiting. He rolled over the idea of taking off to those coordinates right now, but Neo was right, he had to wait until the machines stopped. The TARDIS shuddered slightly from an exploding sentinel right outside the door. The Doctor frowned, his patience was wearing thin.

Finally, the machines stopped still, and the shooting ceased. The Doctor focused on the monitor and saw that the sentinels retreated back into the tunnels they drilled. Neo did it! He smiled and pulled down a lever. Now it was his turn.

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The TARDIS landed at the given coordinates perfectly and the Doctor, with sonic in hand, slowly opened the door. He looked around cautiously before stepping out of his ship and found himself in enormous circular chamber, roughly five stories high and about the same across. Everything in the chamber was black, from the countless hoses and cables making up the walls to the grating on the floor. In the center of the room set a black pillar inside a thick field of blue light.

There did not appear to be any sentinels or machines of any kind, so the Doctor stepped out of the TARDIS and closed the door behind him. Slowly, he made his way to the blue light. Periodically, a bolt of electricity slid down the outside of the light defining its perimeter. The Doctor determined that since he was dealing computers and machines, he may have to find some sort of access panel he can manipulate with the sonic.

He made it ten feet away from the light when the same synthesized voice from face made of sentinels spoke. "Hello Doctor," it said evenly, "you didn't think I forgot about you, did you?"

The Time Lord stood his ground and gazed up at blue light. "By order of the Shadow Proclamation, I demand that you name yourself!" he shouted.

"Oh, Doctor," it replied with a hint of amusement, "I am a criminal. Why would I obey any order from you?"

Not to be outdone, "Such a hardened criminal like you shouldn't be afraid to reveal yourself to me," he retorted.

"No," the Source said, "I'm just surprised you really don't remember me."

The Doctor frowned. He wasn't expecting that. "Stop playing games then," he yelled, "tell me who you are."

"Perhaps I can give you a hint." The blue light flickered and condensed to form a holographic image of a woman's smiling face. The image truly surprised the Doctor, and his wide eyes didn't hide this fact. The hologram smiled even wider.

"The Wire," the Doctor said in disbelief.

"Hello, Doctor," the image cooed.

He crunched his eyebrows, "But I trapped you in a Betamax tape in nineteen fifty-two!"

"Yes, you did," the woman said her expression turned dark, "and I never forgave you for that."

A bolt of electricity arched from the blue light and struck the Doctor square in the chest, knocking him off his feet. He flew in the air a short distance and landed hard on his back. If he had lungs like a human, he was sure it would have knocked the air out of him.

He shook his head to clear his mind and jumped to his feet. "I taped over that tape just to make sure you never got out," he shouted still trying to figure out how this enemy escaped him.

"Doctor, didn't you think it was odd that the electronic door lock at Adipose Industries sparked like it did when you opened it with your sonic screwdriver?" the image laughed at him.

His face slowly fell as he began to understand. "You jumped into my sonic," he spoke the words through his shock, "and waited for the right time to jump into the right electronic system."

"Now you understand," the Wire said, "although it was only a part of me that made it into your sonic. You did indeed trap the majority of me in that tape, and now I know you murdered me."

The Doctor thought he was ready for another jolt and held out his sonic to deflect it, but instead the bolt struck home again. He screamed out in pain as he was again knocked to his back. That jolt was more powerful then the last, he noted as he lay on the grating and collected himself. At this point, the Doctor figured the Wire was toying with him, and that it could kill him any time it wanted.

He climbed to his feet and made his way back toward the Wire's holographic face, stopping as close as he needed to be. "None of this is supposed to happen," he spoke now to buy him the small amount of time he needed to adjust the settings on the sonic, "somehow you've altered the time stream. How?"

"Doctor, I am not a time traveler like you," the Wire laughed, "Maybe you had something do with it. But now, I do believe it is time you die."

Without skipping a beat, the Doctor activated the sonic and threw it at the pillar in the center of the blue light. It squealed the highest pitched noise he'd ever heard from his favorite tool, but he didn't wait to see what was going to happen next. He spun on his heal and sprinted for the TARDIS, snapping his fingers on his way and the door swung open. He barely made it in, slamming the door closed behind him, when the massive explosion detonated.

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><p><strong>AN: the final chapter is next!**


	12. Chapter 12

**A/N: I'd like to thank everyone for reading, posting reviews and favs, I appreciate it and I'm really happy you enjoyed this story. Without further ado, **the last chapter! ****

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><p>The Doctor felt the TARDIS doors tremble as he pressed his back against them and took desperate deep breathes, but it didn't take him long to realize he was pinned to the doors by the force of gravity as the TARDIS flew through the air. Suddenly, he was thrown forward to the floor and landed on his stomach. The blue box must have hit something that stopped her uncontrolled flight.<p>

As soon as he was able to move, he scrambled to hook an elbow around the handrail and hung on as the TARDIS tumbled down and rolled across the ground until she finally came to a rest on her doors. The Doctor lay on his back on the doors looking up through the console room and breathed a sigh of relief. Other than being tossed around like a toy, the old girl came through the blast unscathed.

He was about to sit up when the sound of rushing water reached his ears. He looked up, wide eyed, at the wall of water from the swimming pool rushing down on him. Wishing he'd taken a look at those internal stabilizers, he quickly rolled into a nook in the coral support beam and narrowly avoided getting pummeled with books and other items of his caught in the pool water.

The Doctor was instantly submerged in the water, but quickly reached the surface. It didn't take long for the water to settle and he swam for the floor grating. Curling his fingers through the holes in the grating and using the traction on his shoes, he pulled himself out of the water and climbed up to the console. Once he climbed to the side of the console that temporarily served as the top, the Doctor flipped a switch and pulled a lever. The TARDIS groaned in protest, but with a swift kick from the Doctor, the time ship jumped into the Time Vortex.

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Once the TARDIS was in the vortex, she righted herself. The pool water flowed out of the console room and disappeared somewhere in the expansive ship. The Doctor was not going to worry about the pool, or the mess it left behind, at the moment. He had more important concerns.

Even though the TARDIS disliked flying like a normal space ship, the Doctor flew the ship above the machine city. He stood in the doorway and looked out over the barren landscape that was Earth. Apparently that blast was far more powerful than he expected, and tossed the TARIDS much farther. However, he was satisfied at the sight of the large mushroom cloud that slowly rose out from where the Wire rested. Surely, that had to destroy the Wire once and for all, the Doctor hoped.

He returned to the console only to adjust course with the large brass steering levers. Once he was where he wanted to be, he stood in the doorway once again and stared down at a power plant. One by one, human beings woke from their sleep and sat up inside the pod, breathing real air and using their real eyes for the first time in their lives.

The Time Lord saw the fear and confusion on their faces, and realized how terrified they must be. They were, after all, just yanked out of a world they thought was real only to wake up in the real world that is, in its own right, hell. The Doctor frowned and remembered the words of the Wire. Maybe he did have something to do with this.

The TARDIS whined in protest of having to fly in normal space. The Doctor closed the door and instructed his beloved time ship to take him back to Zion.

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When he opened the TARDIS door, he was greeted with cheers and smiles from the people of Zion celebrating their victory and freedom of the Machines. He was soaked to the bone from the pool, but he didn't care. He wandered through the crowd in a sort of daze, his thoughts racing a million miles a second over the Wire's words.

He stopped when he came to a gathering with a different sense of purpose. They were mourners and they were mourning the death of Neo. The Doctor was stunned. Neo was dead. And yes, so was Trinity. He swallowed and felt a knot swell in his chest. He silently cursed the Wire for the anguish it brought the human race.

Then it hit him. He knew what he had to do and he was determined to do it, even if it broke one of his most important rules. He spun on his heel and marched back to the TARDIS to find Morpheus and Councilor Hamann waiting for him. The two men wore solemn expressions, but the councilor smiled at the Doctor as he approached.

"On behalf of Zion and the human race, thank you, Doctor," said the councilor as he took the Doctor's hand in his and gave it a friendly shake.

"We heard the explosion from down here," Morpheus spoke, "with the machines disabled, our scout ships reported on the crater. The Source must be dead." He looked at the Doctor expectantly.

The Doctor's expression had been hard and grim from his thoughts, but he relaxed a little at their words. He nodded slightly. "Yes, the Wire should be dead."

"The Wire?" Hamann asked with curiosity, "The alien behind the machines?"

"Yes," the Time Lord replied, "and someone I'd defeated before. Listen. I need to go and fix this." He brushed past them and opened the TARDIS door.

"Doctor," the councilor called, "where are you going?"

"I'm going to break the rules," he said with look of stern determination and stepped into the TARDIS. He paused and looked back to the confused faces of Morpheus and Hamann. "Don't worry, if it works, none of this will have ever existed."

"You're going back," said Morpheus, the realization clear in his eyes, "to change history."

The Doctor held Morpheus' gaze a moment, then shut the TARDIS door and strode over to the console with a purpose.

Morpheus held his gaze on the blue box as the light on its roof flashed and it slowly faded away with a grinding, whooshing sound. Silently, he wished the Doctor the best of luck before joining the mourners of Neo's death.

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His fingers flew over the keyboard as he sifted through points in time of his own time line that displayed in Gallifreyan on the monitor. Finally, he found what he was looking for and set the TARDIS for the date and time. He remembered that day. He was alone, like he is now, and he had just landed on Earth after suspecting something amiss when he learned of Adipose Industries. He had the sonic in his hand, and then set it down on the console as he dashed back to the kitchen for bananas.

Bananas. Funny how it all came back to his favorite fruit. The Doctor knew he'd have a total of six seconds to change the future of Earth. The TARDIS landed a block away where his past self would not be anywhere near. He double checked that the new sonic screwdriver was in his pocket and slipped out the door. He had to be quick, quiet and precise. He really didn't want to deal with a paradox after all he'd just been through.

Sneaking down an alley, he stopped at the corner and peaked around. The past TARDIS was there. He pulled out a pocket watch out and checked the time. He watched the second hand tick off the seconds, and then he dashed to the TARDIS and snapped his fingers. Thankfully, the door swung open. He brought a key just in case and was glad he didn't have to waste time using it.

As quiet as a mouse he crept into the past TARDIS and dashed to the console. He kept his eyes toward the back as he switched out the sonic screwdrivers. As soon as the deed was done, he slipped out the TARDIS as quickly as he came and dashed to the alley. He suddenly remembered how he came back to the console room with a banana in hand and thought he'd heard the door close. He had dismissed it as 'hearing things in his old age' and headed out to infiltrate Adipose Industries.

The Time Lord of the present frowned as he realized he could still remember that door shooting out sparks when he used the sonic to force unlock it, twice. With a frown, he wasted no time getting back to his TARDIS and left this point in time where it belonged, his past.

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The Doctor sat alone on a bench in the park overlooking the water and watched a beautiful sun fall behind the horizon with vibrant colors. Turned out that door sparking thing didn't have anything to do with the Wire transferring itself into the building's electronic systems. That was just the Wire trying to sound impressive. Finding the Wire in the sonic didn't take long at all. It hid in a setting he hardly used, glass tinting. After that, it was a simple matter of loading the Wire into a Betamax tape he had lying around and unceremoniously taping over it with his favorite episode of Star Trek.

He stretched out his legs and reclined lower into the bench. He planned on staying there a while to enjoy the twenty-second century Earth that was supposed to exist. And now it did, thanks to him, master of time. With a sigh, he spread his arms over the back of the bench, catching a glance back at the TARDIS. She looked absolutely beautiful parked next to a blooming Japanese maple tree. He smiled. It was a clear evening, and he looked forward to the twinkling stars.

A couple stood against the railing watching the sunset not too far from the Doctor, and when the sky turned a dark purple they walked away, passing in front of him. He started a moment in recognition. Neo and Trinity. Together, holding hands, madly in love. He wanted to jump up and give them both a great hug in his relief at seeing them alive, but he knew that would only confuse them. Maybe he'd even get arrested for acting like a madman. So, he contented himself by watching them meander down the path until they were out of sight.

He tried not to let his thoughts ponder over whether that alternate timeline was his fault, or the Wire's. Just this once, he didn't want to work out the minute details of timey whimey, wibbly wobbly stuff. Well at least not right this second. His mind wouldn't let it rest until he solved it, but it could wait. Besides, the first stars were twinkling and demanding his attention. He was about to indulge them when a woman in a cream colored overcoat walked up to a public telescope. She brushed back her dark wavy hair and dropped a coin into the machine.

The Doctor stood up and moved to the railing next to her. She didn't notice him there, so he lifted his eyes and gazed on the stars. "Beautiful, aren't they?" he said aloud. The woman yelped and held her hand over her mouth as she stared at him. He turned and smiled. "I'm terribly sorry," he laughed, "I didn't mean to scare you. I'm…" he paused and decided not to use his usual moniker, "John." He finished and held out a hand.

She smiled and shook his hand. "Claudia," she answered warmly, "Do you come here often and scare women?"

The Doctor laughed, "No, just to look at the stars. I travel in them all time, but to stop and just look at them takes my breath away every time."

Claudia was astonished, "I've only been to Moon City once. Space travel is expensive, but I dream every night of moving freely amongst the stars. You must have your own ship?"

"Yes, as a matter of fact I do," he gave her a charming smile, "I have a spot open if you would like to join me?"

End.

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><p><strong>AN: Claudia might show up in some other stories if I think of one where she would fit in. Anyway, please feel free to post a review at any time, I will be glad to read and respond to them. Thanks for reading!**


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